diff --git a/R/internal_functions.R b/R/internal_functions.R index a3300c25..35d506e0 100644 --- a/R/internal_functions.R +++ b/R/internal_functions.R @@ -52,9 +52,9 @@ jaspar = switch( arg[[2]], name = "JASPAR", - url = "https://jaspar.genereg.net", + url = "https://jaspar.elixir.no/", pth = "api/v1/", - ptn = "^(https?://)?(www\\.)?jaspar\\.genereg\\.net/api/", + ptn = "^(https?://)?(www\\.)?jaspar\\.elixir\\.no/api/", err_ptn = "^$" ), mieaa = switch( diff --git a/R/jaspar.R b/R/jaspar.R index fef6f89a..17202991 100644 --- a/R/jaspar.R +++ b/R/jaspar.R @@ -6,41 +6,40 @@ #' Using this function, you can retrieve a list of available collections #' in a JASPAR release. #' -#' @param release Numeric: (default = 2022) Which JASPAR database release -#' to use? Available options are: 2014, 2016, 2018, 2020, and 2022. +#' @param release Numeric: (default = 2024) Which JASPAR database release +#' to use? Available options are: 2024, 2022, 2020, 2018, 2016, and 2014. #' @param ... rbioapi option(s). See \code{\link{rba_options}}'s #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.genereg.net/api/v1/collections/" +#' "GET "https://jaspar.elixir.no/api/v1/collections/" #' #' @return A data frame with collections' names and URLs. #' #' @references \itemize{ -#' \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva -#' Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, -#' Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol -#' Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel -#' Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris -#' Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, -#' Anthony Mathelier, JASPAR 2022: the 9th release of the open-access -#' database of transcription factor binding profiles, Nucleic Acids -#' Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, -#' https://doi.org/10.1093/nar/gkab1113 +#' \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, +#' Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, +#' Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard +#' B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: +#' 20th anniversary of the open-access database of transcription factor +#' binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 +#' \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data +#' from any programming language. Bioinformatics, 2017, +#' doi: 10.1093/bioinformatics/btx804 #' \item -#' \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} -#' \item \href{https://jaspar.genereg.net/faq/}{Citations note +#' \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} +#' \item \href{https://jaspar.elixir.no/faq/}{Citations note #' on JASPAR website} #' } #' #' @examples #' \donttest{ -#' rba_jaspar_collections(release = 2022) +#' rba_jaspar_collections(release = 2024) #' } #' #' @family "JASPAR" #' @export -rba_jaspar_collections <- function(release = 2022, +rba_jaspar_collections <- function(release = 2024, ...) { ## Load Global Options .rba_ext_args(...) @@ -48,7 +47,7 @@ rba_jaspar_collections <- function(release = 2022, .rba_args(cons = list(list(arg = "release", class = "numeric", no_null = TRUE, - val = c(2014, 2016, 2018, 2020, 2022)) + val = c(2014, 2016, 2018, 2020, 2022, 2024)) )) .msg("Retrieving a list of collections available in JASPAR release %s.", @@ -88,12 +87,12 @@ rba_jaspar_collections <- function(release = 2022, #' to automatically iterate over multiple pages. #' #' @param collection JASPAR Collection's name. See -#' \href{https://jaspar.genereg.net/docs/}{JASPAR Collections} for +#' \href{https://jaspar.elixir.no/docs/}{JASPAR Collections} for #' information. The accepted values are: "CORE", "CNE", "PHYLOFACTS", #' "SPLICE", "POLII", "FAM", "PBM", "PBM_HOMEO", "PBM_HLH", and #' "UNVALIDATED". -#' @param release Numeric: (default = 2022) Which JASPAR database release -#' to use? Available options are: 2014, 2016, 2018, 2020, and 2022. +#' @param release Numeric: (default = 2024) Which JASPAR database release +#' to use? Available options are: 2024, 2022, 2020, 2018, 2016, and 2014. #' @param only_last_version Logical: (default = FALSE) If TRUE, only the #' latest version of a matrix profile will be returned. #' @param search Character: A search term. @@ -110,32 +109,31 @@ rba_jaspar_collections <- function(release = 2022, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.genereg.net/api/v1/collections/{collection}/" +#' "GET "https://jaspar.elixir.no/api/v1/collections/{collection}/" #' #' @return A list that contains a data frame with information of matrix #' profiles available in the collection. #' #' @references \itemize{ -#' \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva -#' Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, -#' Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol -#' Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel -#' Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris -#' Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, -#' Anthony Mathelier, JASPAR 2022: the 9th release of the open-access -#' database of transcription factor binding profiles, Nucleic Acids -#' Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, -#' https://doi.org/10.1093/nar/gkab1113 +#' \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, +#' Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, +#' Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard +#' B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: +#' 20th anniversary of the open-access database of transcription factor +#' binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 +#' \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data +#' from any programming language. Bioinformatics, 2017, +#' doi: 10.1093/bioinformatics/btx804 #' \item -#' \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} -#' \item \href{https://jaspar.genereg.net/faq/}{Citations note +#' \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} +#' \item \href{https://jaspar.elixir.no/faq/}{Citations note #' on JASPAR website} #' } #' #' @examples #' \donttest{ #' rba_jaspar_collections_matrices(collection = "CORE", -#' release = 2022, +#' release = 2024, #' page_size = 100, #' page = 2) #' } @@ -143,7 +141,7 @@ rba_jaspar_collections <- function(release = 2022, #' @family "JASPAR" #' @export rba_jaspar_collections_matrices <- function(collection, - release = 2022, + release = 2024, only_last_version = FALSE, search = NULL, order = NULL, @@ -170,7 +168,7 @@ rba_jaspar_collections_matrices <- function(collection, list(arg = "release", class = "numeric", no_null = TRUE, - val = c(2014, 2016, 2018, 2020, 2022)), + val = c(2014, 2016, 2018, 2020, 2022, 2024)), list(arg = "search", class = "character"), list(arg = "order", @@ -247,8 +245,8 @@ rba_jaspar_collections_matrices <- function(collection, #' for matrix construction). For example: "ChIP-seq", "PBM" #' @param collection Character: JASPAR matrix profile collection name. USE #' \code{\link{rba_jaspar_collections}} to get a list of collection names. -#' @param release Numeric: (default = 2022) Which JASPAR database release -#' to use? Available options are: 2014, 2016, 2018, 2020, and 2022. +#' @param release Numeric: (default = 2024) Which JASPAR database release +#' to use? Available options are: 2024, 2022, 2020, 2018, 2016, and 2014. #' @param only_last_version Logical: (default = FALSE) If TRUE, only the #' latest version of a matrix profile will be returned. #' @param order Character: A character string or a vector of character strings @@ -264,24 +262,23 @@ rba_jaspar_collections_matrices <- function(collection, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.genereg.net/api/v1/api/v1/matrix/" +#' "GET "https://jaspar.elixir.no/api/v1/api/v1/matrix/" #' #' @return A list that contains a data frame of matrix profiles' information. #' #' @references \itemize{ -#' \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva -#' Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, -#' Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol -#' Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel -#' Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris -#' Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, -#' Anthony Mathelier, JASPAR 2022: the 9th release of the open-access -#' database of transcription factor binding profiles, Nucleic Acids -#' Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, -#' https://doi.org/10.1093/nar/gkab1113 +#' \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, +#' Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, +#' Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard +#' B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: +#' 20th anniversary of the open-access database of transcription factor +#' binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 +#' \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data +#' from any programming language. Bioinformatics, 2017, +#' doi: 10.1093/bioinformatics/btx804 #' \item -#' \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} -#' \item \href{https://jaspar.genereg.net/faq/}{Citations note +#' \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} +#' \item \href{https://jaspar.elixir.no/faq/}{Citations note #' on JASPAR website} #' } #' @@ -305,7 +302,7 @@ rba_jaspar_matrix_search <- function(term = NULL, tax_id = NULL, data_type = NULL, collection = NULL, - release = 2022, + release = 2024, only_last_version = FALSE, order = NULL, page_size = 1000, @@ -343,7 +340,7 @@ rba_jaspar_matrix_search <- function(term = NULL, list(arg = "release", class = "numeric", no_null = TRUE, - val = c(2014, 2016, 2018, 2020, 2022)), + val = c(2014, 2016, 2018, 2020, 2022, 2024)), list(arg = "order", class = "character"), list(arg = "only_last_version", @@ -432,24 +429,23 @@ rba_jaspar_matrix_search <- function(term = NULL, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.genereg.net/api/v1/matrix/{base_id}/versions/" +#' "GET "https://jaspar.elixir.no/api/v1/matrix/{base_id}/versions/" #' #' @return A data frame of matrix profiles' versions information. #' #' @references \itemize{ -#' \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva -#' Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, -#' Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol -#' Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel -#' Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris -#' Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, -#' Anthony Mathelier, JASPAR 2022: the 9th release of the open-access -#' database of transcription factor binding profiles, Nucleic Acids -#' Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, -#' https://doi.org/10.1093/nar/gkab1113 +#' \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, +#' Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, +#' Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard +#' B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: +#' 20th anniversary of the open-access database of transcription factor +#' binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 +#' \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data +#' from any programming language. Bioinformatics, 2017, +#' doi: 10.1093/bioinformatics/btx804 #' \item -#' \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} -#' \item \href{https://jaspar.genereg.net/faq/}{Citations note +#' \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} +#' \item \href{https://jaspar.elixir.no/faq/}{Citations note #' on JASPAR website} #' } #' @@ -524,26 +520,25 @@ rba_jaspar_matrix_versions <- function(base_id, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.genereg.net/api/v1/matrix/{matrix_id}/" +#' "GET "https://jaspar.elixir.no/api/v1/matrix/{matrix_id}/" #' #' @return A list that contains the PFM along with its details and #' annotations. If file_format was supplied, an un-parsed character string #' with the file's content. #' #' @references \itemize{ -#' \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva -#' Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, -#' Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol -#' Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel -#' Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris -#' Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, -#' Anthony Mathelier, JASPAR 2022: the 9th release of the open-access -#' database of transcription factor binding profiles, Nucleic Acids -#' Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, -#' https://doi.org/10.1093/nar/gkab1113 +#' \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, +#' Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, +#' Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard +#' B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: +#' 20th anniversary of the open-access database of transcription factor +#' binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 +#' \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data +#' from any programming language. Bioinformatics, 2017, +#' doi: 10.1093/bioinformatics/btx804 #' \item -#' \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} -#' \item \href{https://jaspar.genereg.net/faq/}{Citations note +#' \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} +#' \item \href{https://jaspar.elixir.no/faq/}{Citations note #' on JASPAR website} #' } #' @@ -643,26 +638,25 @@ rba_jaspar_matrix <- function(matrix_id, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.genereg.net/api/v1/releases/" -#' "GET "https://jaspar.genereg.net/api/v1/releases/{release_number}/" +#' "GET "https://jaspar.elixir.no/api/v1/releases/" +#' "GET "https://jaspar.elixir.no/api/v1/releases/{release_number}/" #' #' @return A list that contains all JASPAR database releases' information or #' details of a particular release. #' #' @references \itemize{ -#' \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva -#' Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, -#' Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol -#' Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel -#' Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris -#' Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, -#' Anthony Mathelier, JASPAR 2022: the 9th release of the open-access -#' database of transcription factor binding profiles, Nucleic Acids -#' Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, -#' https://doi.org/10.1093/nar/gkab1113 +#' \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, +#' Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, +#' Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard +#' B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: +#' 20th anniversary of the open-access database of transcription factor +#' binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 +#' \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data +#' from any programming language. Bioinformatics, 2017, +#' doi: 10.1093/bioinformatics/btx804 #' \item -#' \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} -#' \item \href{https://jaspar.genereg.net/faq/}{Citations note +#' \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} +#' \item \href{https://jaspar.elixir.no/faq/}{Citations note #' on JASPAR website} #' } #' @@ -737,24 +731,23 @@ rba_jaspar_releases <- function(release_number = NULL, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.genereg.net/api/v1/sites/{matrix_id}/" +#' "GET "https://jaspar.elixir.no/api/v1/sites/{matrix_id}/" #' #' @return A list that contains a data frame with binding sites information. #' #' @references \itemize{ -#' \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva -#' Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, -#' Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol -#' Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel -#' Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris -#' Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, -#' Anthony Mathelier, JASPAR 2022: the 9th release of the open-access -#' database of transcription factor binding profiles, Nucleic Acids -#' Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, -#' https://doi.org/10.1093/nar/gkab1113 +#' \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, +#' Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, +#' Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard +#' B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: +#' 20th anniversary of the open-access database of transcription factor +#' binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 +#' \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data +#' from any programming language. Bioinformatics, 2017, +#' doi: 10.1093/bioinformatics/btx804 #' \item -#' \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} -#' \item \href{https://jaspar.genereg.net/faq/}{Citations note +#' \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} +#' \item \href{https://jaspar.elixir.no/faq/}{Citations note #' on JASPAR website} #' } #' @@ -805,8 +798,8 @@ rba_jaspar_sites <- function(matrix_id, #' in six taxonomic groups. Use this function to retrieve a list of #' available species in a JASPAR database release. #' -#' @param release Numeric: (default = 2022) Which JASPAR database release -#' to use? Available options are: 2014, 2016, 2018, 2020, and 2022. +#' @param release Numeric: (default = 2024) Which JASPAR database release +#' to use? Available options are: 2024, 2022, 2020, 2018, 2016, and 2014. #' @param search Character: A search term. #' @param order Character: A character string or a vector of character strings #' of field names that will be used to order the results. @@ -816,35 +809,34 @@ rba_jaspar_sites <- function(matrix_id, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.genereg.net/api/v1/species/" +#' "GET "https://jaspar.elixir.no/api/v1/species/" #' #' @return A data frame with information of available species. #' #' @references \itemize{ -#' \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva -#' Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, -#' Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol -#' Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel -#' Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris -#' Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, -#' Anthony Mathelier, JASPAR 2022: the 9th release of the open-access -#' database of transcription factor binding profiles, Nucleic Acids -#' Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, -#' https://doi.org/10.1093/nar/gkab1113 +#' \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, +#' Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, +#' Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard +#' B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: +#' 20th anniversary of the open-access database of transcription factor +#' binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 +#' \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data +#' from any programming language. Bioinformatics, 2017, +#' doi: 10.1093/bioinformatics/btx804 #' \item -#' \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} -#' \item \href{https://jaspar.genereg.net/faq/}{Citations note +#' \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} +#' \item \href{https://jaspar.elixir.no/faq/}{Citations note #' on JASPAR website} #' } #' #' @examples #' \donttest{ -#' rba_jaspar_species(release = 2022) +#' rba_jaspar_species(release = 2024) #' } #' #' @family "JASPAR" #' @export -rba_jaspar_species <- function(release = 2022, +rba_jaspar_species <- function(release = 2024, search = NULL, order = NULL, ...) { @@ -854,7 +846,7 @@ rba_jaspar_species <- function(release = 2022, .rba_args(cons = list(list(arg = "release", class = "numeric", no_null = TRUE, - val = c(2014, 2016, 2018, 2020, 2022)), + val = c(2014, 2016, 2018, 2020, 2022, 2024)), list(arg = "search", class = "character"), list(arg = "order", @@ -908,8 +900,8 @@ rba_jaspar_species <- function(release = 2022, #' #' @param tax_id Numeric: NCBI taxonomic Identifier of species. Use #' \code{\link{rba_jaspar_species}} to get a list of supported Species. -#' @param release Numeric: (default = 2022) Which JASPAR database release -#' to use? Available options are: 2014, 2016, 2018, 2020, and 2022. +#' @param release Numeric: (default = 2024) Which JASPAR database release +#' to use? Available options are: 2024, 2022, 2020, 2018, 2016, and 2014. #' @param only_last_version Logical: (default = FALSE) If TRUE, only the #' latest version of a matrix profile will be returned. #' @param search Character: A search term. @@ -926,25 +918,24 @@ rba_jaspar_species <- function(release = 2022, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.genereg.net/api/v1/species/{tax_id}/" +#' "GET "https://jaspar.elixir.no/api/v1/species/{tax_id}/" #' #' @return A list that contains a data frame with information of matrix #' profiles available for the species. #' #' @references \itemize{ -#' \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva -#' Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, -#' Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol -#' Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel -#' Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris -#' Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, -#' Anthony Mathelier, JASPAR 2022: the 9th release of the open-access -#' database of transcription factor binding profiles, Nucleic Acids -#' Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, -#' https://doi.org/10.1093/nar/gkab1113 +#' \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, +#' Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, +#' Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard +#' B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: +#' 20th anniversary of the open-access database of transcription factor +#' binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 +#' \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data +#' from any programming language. Bioinformatics, 2017, +#' doi: 10.1093/bioinformatics/btx804 #' \item -#' \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} -#' \item \href{https://jaspar.genereg.net/faq/}{Citations note +#' \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} +#' \item \href{https://jaspar.elixir.no/faq/}{Citations note #' on JASPAR website} #' } #' @@ -956,7 +947,7 @@ rba_jaspar_species <- function(release = 2022, #' @family "JASPAR" #' @export rba_jaspar_species_matrices <- function(tax_id, - release = 2022, + release = 2024, only_last_version = FALSE, search = NULL, order = NULL, @@ -971,7 +962,7 @@ rba_jaspar_species_matrices <- function(tax_id, list(arg = "release", class = "numeric", no_null = TRUE, - val = c(2014, 2016, 2018, 2020, 2022)), + val = c(2014, 2016, 2018, 2020, 2022, 2024)), list(arg = "only_last_version", class = "logical"), list(arg = "search", @@ -1029,41 +1020,40 @@ rba_jaspar_species_matrices <- function(tax_id, #' in six taxonomic groups. Use this function to retrieve a list of #' available taxonomic groups in a JASPAR database release. #' -#' @param release Numeric: (default = 2022) Which JASPAR database release -#' to use? Available options are: 2014, 2016, 2018, 2020, and 2022. +#' @param release Numeric: (default = 2024) Which JASPAR database release +#' to use? Available options are: 2024, 2022, 2020, 2018, 2016, and 2014. #' @param ... rbioapi option(s). See \code{\link{rba_options}}'s #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.genereg.net/api/v1/taxon/" +#' "GET "https://jaspar.elixir.no/api/v1/taxon/" #' #' @return A data frame with information of available species. #' #' @references \itemize{ -#' \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva -#' Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, -#' Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol -#' Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel -#' Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris -#' Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, -#' Anthony Mathelier, JASPAR 2022: the 9th release of the open-access -#' database of transcription factor binding profiles, Nucleic Acids -#' Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, -#' https://doi.org/10.1093/nar/gkab1113 +#' \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, +#' Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, +#' Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard +#' B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: +#' 20th anniversary of the open-access database of transcription factor +#' binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 +#' \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data +#' from any programming language. Bioinformatics, 2017, +#' doi: 10.1093/bioinformatics/btx804 #' \item -#' \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} -#' \item \href{https://jaspar.genereg.net/faq/}{Citations note +#' \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} +#' \item \href{https://jaspar.elixir.no/faq/}{Citations note #' on JASPAR website} #' } #' #' @examples #' \donttest{ -#' rba_jaspar_taxons(release = 2022) +#' rba_jaspar_taxons(release = 2024) #' } #' #' @family "JASPAR" #' @export -rba_jaspar_taxons <- function(release = 2022, +rba_jaspar_taxons <- function(release = 2024, ...) { ## Load Global Options .rba_ext_args(...) @@ -1071,7 +1061,7 @@ rba_jaspar_taxons <- function(release = 2022, .rba_args(cons = list(list(arg = "release", class = "numeric", no_null = TRUE, - val = c(2014, 2016, 2018, 2020, 2022)) + val = c(2014, 2016, 2018, 2020, 2022, 2024)) )) .msg("Retrieving a list of taxonomic groups available in JASPAR release %s.", @@ -1114,8 +1104,8 @@ rba_jaspar_taxons <- function(release = 2022, #' @param tax_group Character: Taxonomic group. Use #' \code{\link{rba_jaspar_taxons}} to get a list of supported Taxonomic #' groups. -#' @param release Numeric: (default = 2022) Which JASPAR database release -#' to use? Available options are: 2014, 2016, 2018, 2020, and 2022. +#' @param release Numeric: (default = 2024) Which JASPAR database release +#' to use? Available options are: 2024, 2022, 2020, 2018, 2016, and 2014. #' @param only_last_version Logical: (default = FALSE) If TRUE, only the #' latest version of a matrix profile will be returned. #' @param search Character: A search term. @@ -1132,25 +1122,24 @@ rba_jaspar_taxons <- function(release = 2022, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.genereg.net/api/v1/taxon/{tax_group}/" +#' "GET "https://jaspar.elixir.no/api/v1/taxon/{tax_group}/" #' #' @return A list that contains a data frame with information of matrix #' profiles available for the taxonomic group. #' #' @references \itemize{ -#' \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva -#' Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, -#' Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol -#' Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel -#' Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris -#' Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, -#' Anthony Mathelier, JASPAR 2022: the 9th release of the open-access -#' database of transcription factor binding profiles, Nucleic Acids -#' Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, -#' https://doi.org/10.1093/nar/gkab1113 +#' \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, +#' Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, +#' Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard +#' B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: +#' 20th anniversary of the open-access database of transcription factor +#' binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 +#' \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data +#' from any programming language. Bioinformatics, 2017, +#' doi: 10.1093/bioinformatics/btx804 #' \item -#' \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} -#' \item \href{https://jaspar.genereg.net/faq/}{Citations note +#' \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} +#' \item \href{https://jaspar.elixir.no/faq/}{Citations note #' on JASPAR website} #' } #' @@ -1162,7 +1151,7 @@ rba_jaspar_taxons <- function(release = 2022, #' @family "JASPAR" #' @export rba_jaspar_taxons_matrices <- function(tax_group, - release = 2022, + release = 2024, only_last_version = FALSE, search = NULL, order = NULL, @@ -1186,7 +1175,7 @@ rba_jaspar_taxons_matrices <- function(tax_group, list(arg = "release", class = "numeric", no_null = TRUE, - val = c(2014, 2016, 2018, 2020, 2022)), + val = c(2014, 2016, 2018, 2020, 2022, 2024)), list(arg = "only_last_version", class = "logical"), list(arg = "search", @@ -1253,8 +1242,8 @@ rba_jaspar_taxons_matrices <- function(tax_group, #' to automatically iterate over multiple pages. #' #' @param term Character: A search term. -#' @param release Numeric: (default = 2022) Which JASPAR database release -#' to use? Available options are: 2014, 2016, 2018, 2020, and 2022. +#' @param release Numeric: (default = 2024) Which JASPAR database release +#' to use? Available options are: 2024, 2022, 2020, 2018, 2016, and 2014. #' @param tax_group Character: Taxonomic group. Use #' \code{\link{rba_jaspar_taxons}} to get a list of supported Taxonomic #' groups. @@ -1272,25 +1261,24 @@ rba_jaspar_taxons_matrices <- function(tax_group, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.genereg.net/api/v1/api/v1/tffm/" +#' "GET "https://jaspar.elixir.no/api/v1/api/v1/tffm/" #' #' @return A list that contains a data frame with information of query hits' #' TFFMs. #' #' @references \itemize{ -#' \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva -#' Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, -#' Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol -#' Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel -#' Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris -#' Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, -#' Anthony Mathelier, JASPAR 2022: the 9th release of the open-access -#' database of transcription factor binding profiles, Nucleic Acids -#' Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, -#' https://doi.org/10.1093/nar/gkab1113 +#' \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, +#' Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, +#' Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard +#' B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: +#' 20th anniversary of the open-access database of transcription factor +#' binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 +#' \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data +#' from any programming language. Bioinformatics, 2017, +#' doi: 10.1093/bioinformatics/btx804 #' \item -#' \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} -#' \item \href{https://jaspar.genereg.net/faq/}{Citations note +#' \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} +#' \item \href{https://jaspar.elixir.no/faq/}{Citations note #' on JASPAR website} #' } #' @@ -1304,7 +1292,7 @@ rba_jaspar_taxons_matrices <- function(tax_group, #' @family "JASPAR" #' @export rba_jaspar_tffm_search <- function(term = NULL, - release = 2022, + release = 2024, tax_group = NULL, search = NULL, order = NULL, @@ -1319,7 +1307,7 @@ rba_jaspar_tffm_search <- function(term = NULL, list(arg = "release", class = "numeric", no_null = TRUE, - val = c(2014, 2016, 2018, 2020, 2022)), + val = c(2014, 2016, 2018, 2020, 2022, 2024)), list(arg = "tax_group", class = "character", val = c("plants", @@ -1388,24 +1376,23 @@ rba_jaspar_tffm_search <- function(term = NULL, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.genereg.net/api/v1/fttm/{tffm_id}/" +#' "GET "https://jaspar.elixir.no/api/v1/fttm/{tffm_id}/" #' #' @return A list that contains the TFFM's information and annotations. #' #' @references \itemize{ -#' \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva -#' Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, -#' Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol -#' Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel -#' Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris -#' Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, -#' Anthony Mathelier, JASPAR 2022: the 9th release of the open-access -#' database of transcription factor binding profiles, Nucleic Acids -#' Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, -#' https://doi.org/10.1093/nar/gkab1113 +#' \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, +#' Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, +#' Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard +#' B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: +#' 20th anniversary of the open-access database of transcription factor +#' binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 +#' \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data +#' from any programming language. Bioinformatics, 2017, +#' doi: 10.1093/bioinformatics/btx804 #' \item -#' \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} -#' \item \href{https://jaspar.genereg.net/faq/}{Citations note +#' \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} +#' \item \href{https://jaspar.elixir.no/faq/}{Citations note #' on JASPAR website} #' } #' diff --git a/README.Rmd b/README.Rmd index e391fb1c..87427c61 100644 --- a/README.Rmd +++ b/README.Rmd @@ -46,7 +46,7 @@ rbioapi is dedicated to **Biological or Medical** databases and web services. Cu On CRAN (Stable) version: () 1. [Enrichr](https://maayanlab.cloud/Enrichr/ "Enrichr") ([rbioapi vignette article](https://rbioapi.moosa-r.com/articles/rbioapi_enrichr.html "rbioapi & Enrichr vignette article")) ^(new)^ -2. [JASPAR](https://jaspar.genereg.net/ "JASPAR - A database of transcription factor binding profiles") ([rbioapi vignette article](https://rbioapi.moosa-r.com/articles/rbioapi_jaspar.html "rbioapi & Enrichr vignette article")) ^(new)^ +2. [JASPAR](https://jaspar.elixir.no/ "JASPAR - A database of transcription factor binding profiles") ([rbioapi vignette article](https://rbioapi.moosa-r.com/articles/rbioapi_jaspar.html "rbioapi & Enrichr vignette article")) ^(new)^ 3. [miEAA](https://ccb-compute2.cs.uni-saarland.de/mieaa2 "miRNA Enrichment Analysis and Annotation Tool (miEAA)") ([rbioapi vignette article](https://rbioapi.moosa-r.com/articles/rbioapi_mieaa.html "rbioapi & miEAA vignette article")) 4. [PANTHER](https://www.pantherdb.org "Protein Analysis THrough Evolutionary Relationships (PANTHER)") ([rbioapi vignette article](https://rbioapi.moosa-r.com/articles/rbioapi_panther.html "rbioapi & PANTHER vignette article")) 5. [Reactome](https://reactome.org/) ([rbioapi vignette article](https://rbioapi.moosa-r.com/articles/rbioapi_reactome.html "rbioapi & Reactome vignette article")) @@ -200,7 +200,7 @@ rbioapi is an interface between you and other databases and services. Thus, if y - [How to cite Enrichr](https://rbioapi.moosa-r.com/articles/rbioapi_enrichr.html#citations "How to cite Enrichr"). (See on [Enrichr website](https://maayanlab.cloud/Enrichr/help#terms)) -- [How to cite JASPAR](https://rbioapi.moosa-r.com/articles/rbioapi_jaspar.html#citations "How to cite JASPAR"). (See on [JASPAR website](https://jaspar.genereg.net/faq/)) +- [How to cite JASPAR](https://rbioapi.moosa-r.com/articles/rbioapi_jaspar.html#citations "How to cite JASPAR"). (See on [JASPAR website](https://jaspar.elixir.no/faq/)) - [How to cite miEAA](https://rbioapi.moosa-r.com/articles/rbioapi_mieaa.html#citations "How to cite miEAA"). (See on [miEAA website](https://ccb-compute2.cs.uni-saarland.de/mieaa2)) diff --git a/README.md b/README.md index c883fcfb..2c577eaa 100644 --- a/README.md +++ b/README.md @@ -44,7 +44,7 @@ On CRAN (Stable) version: () vignette article](https://rbioapi.moosa-r.com/articles/rbioapi_enrichr.html "rbioapi & Enrichr vignette article")) (new) -2. [JASPAR](https://jaspar.genereg.net/ "JASPAR - A database of transcription factor binding profiles") +2. [JASPAR](https://jaspar.elixir.no/ "JASPAR - A database of transcription factor binding profiles") ([rbioapi vignette article](https://rbioapi.moosa-r.com/articles/rbioapi_jaspar.html "rbioapi & Enrichr vignette article")) (new) @@ -339,7 +339,7 @@ used. - [How to cite JASPAR](https://rbioapi.moosa-r.com/articles/rbioapi_jaspar.html#citations "How to cite JASPAR"). (See on - [JASPAR website](https://jaspar.genereg.net/faq/)) + [JASPAR website](https://jaspar.elixir.no/faq/)) - [How to cite miEAA](https://rbioapi.moosa-r.com/articles/rbioapi_mieaa.html#citations "How to cite miEAA"). (See on [miEAA diff --git a/_pkgdown.yml b/_pkgdown.yml index 45256db7..8b491e53 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -90,7 +90,7 @@ reference: - title: JASPAR (rba_jaspar_*) desc: > - Functions that connect you to [JASPAR](https://jaspar.genereg.net/) + Functions that connect you to [JASPAR](https://jaspar.elixir.no/) (Database of transcription factor binding profiles) API resources. contents: - starts_with("rba_jaspar") diff --git a/man/rba_jaspar_collections.Rd b/man/rba_jaspar_collections.Rd index f28c3376..75e9da55 100644 --- a/man/rba_jaspar_collections.Rd +++ b/man/rba_jaspar_collections.Rd @@ -4,11 +4,11 @@ \alias{rba_jaspar_collections} \title{List collections available in JASPAR} \usage{ -rba_jaspar_collections(release = 2022, ...) +rba_jaspar_collections(release = 2024, ...) } \arguments{ -\item{release}{Numeric: (default = 2022) Which JASPAR database release -to use? Available options are: 2014, 2016, 2018, 2020, and 2022.} +\item{release}{Numeric: (default = 2024) Which JASPAR database release +to use? Available options are: 2024, 2022, 2020, 2018, 2016, and 2014.} \item{...}{rbioapi option(s). See \code{\link{rba_options}}'s arguments manual for more information on available options.} @@ -23,30 +23,29 @@ JASPAR organizes matrix profiles into collections. } \section{Corresponding API Resources}{ - "GET "https://jaspar.genereg.net/api/v1/collections/" + "GET "https://jaspar.elixir.no/api/v1/collections/" } \examples{ \donttest{ -rba_jaspar_collections(release = 2022) +rba_jaspar_collections(release = 2024) } } \references{ \itemize{ - \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva - Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, - Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol - Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel - Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris - Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, - Anthony Mathelier, JASPAR 2022: the 9th release of the open-access - database of transcription factor binding profiles, Nucleic Acids - Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, - https://doi.org/10.1093/nar/gkab1113 + \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, + Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, + Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard + B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: + 20th anniversary of the open-access database of transcription factor + binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 + \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data + from any programming language. Bioinformatics, 2017, + doi: 10.1093/bioinformatics/btx804 \item - \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} - \item \href{https://jaspar.genereg.net/faq/}{Citations note + \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} + \item \href{https://jaspar.elixir.no/faq/}{Citations note on JASPAR website} } } diff --git a/man/rba_jaspar_collections_matrices.Rd b/man/rba_jaspar_collections_matrices.Rd index 90ee2540..f28a0f19 100644 --- a/man/rba_jaspar_collections_matrices.Rd +++ b/man/rba_jaspar_collections_matrices.Rd @@ -6,7 +6,7 @@ \usage{ rba_jaspar_collections_matrices( collection, - release = 2022, + release = 2024, only_last_version = FALSE, search = NULL, order = NULL, @@ -17,13 +17,13 @@ rba_jaspar_collections_matrices( } \arguments{ \item{collection}{JASPAR Collection's name. See -\href{https://jaspar.genereg.net/docs/}{JASPAR Collections} for +\href{https://jaspar.elixir.no/docs/}{JASPAR Collections} for information. The accepted values are: "CORE", "CNE", "PHYLOFACTS", "SPLICE", "POLII", "FAM", "PBM", "PBM_HOMEO", "PBM_HLH", and "UNVALIDATED".} -\item{release}{Numeric: (default = 2022) Which JASPAR database release -to use? Available options are: 2014, 2016, 2018, 2020, and 2022.} +\item{release}{Numeric: (default = 2024) Which JASPAR database release +to use? Available options are: 2024, 2022, 2020, 2018, 2016, and 2014.} \item{only_last_version}{Logical: (default = FALSE) If TRUE, only the latest version of a matrix profile will be returned.} @@ -60,13 +60,13 @@ The results are paginated. You can control the page's size number } \section{Corresponding API Resources}{ - "GET "https://jaspar.genereg.net/api/v1/collections/{collection}/" + "GET "https://jaspar.elixir.no/api/v1/collections/{collection}/" } \examples{ \donttest{ rba_jaspar_collections_matrices(collection = "CORE", - release = 2022, + release = 2024, page_size = 100, page = 2) } @@ -74,19 +74,18 @@ rba_jaspar_collections_matrices(collection = "CORE", } \references{ \itemize{ - \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva - Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, - Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol - Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel - Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris - Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, - Anthony Mathelier, JASPAR 2022: the 9th release of the open-access - database of transcription factor binding profiles, Nucleic Acids - Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, - https://doi.org/10.1093/nar/gkab1113 + \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, + Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, + Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard + B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: + 20th anniversary of the open-access database of transcription factor + binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 + \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data + from any programming language. Bioinformatics, 2017, + doi: 10.1093/bioinformatics/btx804 \item - \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} - \item \href{https://jaspar.genereg.net/faq/}{Citations note + \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} + \item \href{https://jaspar.elixir.no/faq/}{Citations note on JASPAR website} } } diff --git a/man/rba_jaspar_matrix.Rd b/man/rba_jaspar_matrix.Rd index 3169c2ba..567bd310 100644 --- a/man/rba_jaspar_matrix.Rd +++ b/man/rba_jaspar_matrix.Rd @@ -35,7 +35,7 @@ Using this function you can retrieve a Position Frequency Matrices (PFM) } \section{Corresponding API Resources}{ - "GET "https://jaspar.genereg.net/api/v1/matrix/{matrix_id}/" + "GET "https://jaspar.elixir.no/api/v1/matrix/{matrix_id}/" } \examples{ @@ -51,19 +51,18 @@ rba_jaspar_matrix(matrix_id = "MA0600.2", } \references{ \itemize{ - \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva - Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, - Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol - Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel - Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris - Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, - Anthony Mathelier, JASPAR 2022: the 9th release of the open-access - database of transcription factor binding profiles, Nucleic Acids - Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, - https://doi.org/10.1093/nar/gkab1113 + \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, + Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, + Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard + B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: + 20th anniversary of the open-access database of transcription factor + binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 + \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data + from any programming language. Bioinformatics, 2017, + doi: 10.1093/bioinformatics/btx804 \item - \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} - \item \href{https://jaspar.genereg.net/faq/}{Citations note + \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} + \item \href{https://jaspar.elixir.no/faq/}{Citations note on JASPAR website} } } diff --git a/man/rba_jaspar_matrix_search.Rd b/man/rba_jaspar_matrix_search.Rd index c7e36a79..9deb2dbc 100644 --- a/man/rba_jaspar_matrix_search.Rd +++ b/man/rba_jaspar_matrix_search.Rd @@ -13,7 +13,7 @@ rba_jaspar_matrix_search( tax_id = NULL, data_type = NULL, collection = NULL, - release = 2022, + release = 2024, only_last_version = FALSE, order = NULL, page_size = 1000, @@ -43,8 +43,8 @@ for matrix construction). For example: "ChIP-seq", "PBM"} \item{collection}{Character: JASPAR matrix profile collection name. USE \code{\link{rba_jaspar_collections}} to get a list of collection names.} -\item{release}{Numeric: (default = 2022) Which JASPAR database release -to use? Available options are: 2014, 2016, 2018, 2020, and 2022.} +\item{release}{Numeric: (default = 2024) Which JASPAR database release +to use? Available options are: 2024, 2022, 2020, 2018, 2016, and 2014.} \item{only_last_version}{Logical: (default = FALSE) If TRUE, only the latest version of a matrix profile will be returned.} @@ -83,7 +83,7 @@ Note that this is a search function. Thus, you are not required to fill } \section{Corresponding API Resources}{ - "GET "https://jaspar.genereg.net/api/v1/api/v1/matrix/" + "GET "https://jaspar.elixir.no/api/v1/api/v1/matrix/" } \examples{ @@ -99,19 +99,18 @@ rba_jaspar_matrix_search(page_size = 100) } \references{ \itemize{ - \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva - Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, - Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol - Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel - Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris - Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, - Anthony Mathelier, JASPAR 2022: the 9th release of the open-access - database of transcription factor binding profiles, Nucleic Acids - Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, - https://doi.org/10.1093/nar/gkab1113 + \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, + Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, + Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard + B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: + 20th anniversary of the open-access database of transcription factor + binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 + \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data + from any programming language. Bioinformatics, 2017, + doi: 10.1093/bioinformatics/btx804 \item - \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} - \item \href{https://jaspar.genereg.net/faq/}{Citations note + \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} + \item \href{https://jaspar.elixir.no/faq/}{Citations note on JASPAR website} } } diff --git a/man/rba_jaspar_matrix_versions.Rd b/man/rba_jaspar_matrix_versions.Rd index 42ab203c..5895efec 100644 --- a/man/rba_jaspar_matrix_versions.Rd +++ b/man/rba_jaspar_matrix_versions.Rd @@ -29,7 +29,7 @@ Since JASPAR release 2010, the matrix profiles } \section{Corresponding API Resources}{ - "GET "https://jaspar.genereg.net/api/v1/matrix/{base_id}/versions/" + "GET "https://jaspar.elixir.no/api/v1/matrix/{base_id}/versions/" } \examples{ @@ -40,19 +40,18 @@ rba_jaspar_matrix_versions("MA0600") } \references{ \itemize{ - \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva - Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, - Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol - Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel - Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris - Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, - Anthony Mathelier, JASPAR 2022: the 9th release of the open-access - database of transcription factor binding profiles, Nucleic Acids - Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, - https://doi.org/10.1093/nar/gkab1113 + \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, + Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, + Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard + B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: + 20th anniversary of the open-access database of transcription factor + binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 + \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data + from any programming language. Bioinformatics, 2017, + doi: 10.1093/bioinformatics/btx804 \item - \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} - \item \href{https://jaspar.genereg.net/faq/}{Citations note + \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} + \item \href{https://jaspar.elixir.no/faq/}{Citations note on JASPAR website} } } diff --git a/man/rba_jaspar_releases.Rd b/man/rba_jaspar_releases.Rd index 46c77af8..16938d39 100644 --- a/man/rba_jaspar_releases.Rd +++ b/man/rba_jaspar_releases.Rd @@ -25,8 +25,8 @@ If a release number was supplied, this function will return the details } \section{Corresponding API Resources}{ -"GET "https://jaspar.genereg.net/api/v1/releases/" - "GET "https://jaspar.genereg.net/api/v1/releases/{release_number}/" +"GET "https://jaspar.elixir.no/api/v1/releases/" + "GET "https://jaspar.elixir.no/api/v1/releases/{release_number}/" } \examples{ @@ -38,19 +38,18 @@ rba_jaspar_releases(7) } \references{ \itemize{ - \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva - Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, - Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol - Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel - Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris - Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, - Anthony Mathelier, JASPAR 2022: the 9th release of the open-access - database of transcription factor binding profiles, Nucleic Acids - Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, - https://doi.org/10.1093/nar/gkab1113 + \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, + Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, + Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard + B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: + 20th anniversary of the open-access database of transcription factor + binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 + \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data + from any programming language. Bioinformatics, 2017, + doi: 10.1093/bioinformatics/btx804 \item - \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} - \item \href{https://jaspar.genereg.net/faq/}{Citations note + \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} + \item \href{https://jaspar.elixir.no/faq/}{Citations note on JASPAR website} } } diff --git a/man/rba_jaspar_sites.Rd b/man/rba_jaspar_sites.Rd index 4903a74c..20a94c63 100644 --- a/man/rba_jaspar_sites.Rd +++ b/man/rba_jaspar_sites.Rd @@ -22,7 +22,7 @@ Use this function to retrieve a list of transcription factor binding sites } \section{Corresponding API Resources}{ - "GET "https://jaspar.genereg.net/api/v1/sites/{matrix_id}/" + "GET "https://jaspar.elixir.no/api/v1/sites/{matrix_id}/" } \examples{ @@ -33,19 +33,18 @@ rba_jaspar_sites("MA0600.1") } \references{ \itemize{ - \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva - Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, - Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol - Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel - Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris - Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, - Anthony Mathelier, JASPAR 2022: the 9th release of the open-access - database of transcription factor binding profiles, Nucleic Acids - Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, - https://doi.org/10.1093/nar/gkab1113 + \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, + Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, + Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard + B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: + 20th anniversary of the open-access database of transcription factor + binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 + \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data + from any programming language. Bioinformatics, 2017, + doi: 10.1093/bioinformatics/btx804 \item - \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} - \item \href{https://jaspar.genereg.net/faq/}{Citations note + \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} + \item \href{https://jaspar.elixir.no/faq/}{Citations note on JASPAR website} } } diff --git a/man/rba_jaspar_species.Rd b/man/rba_jaspar_species.Rd index 296fe114..292a4525 100644 --- a/man/rba_jaspar_species.Rd +++ b/man/rba_jaspar_species.Rd @@ -4,11 +4,11 @@ \alias{rba_jaspar_species} \title{List available species in JASPAR} \usage{ -rba_jaspar_species(release = 2022, search = NULL, order = NULL, ...) +rba_jaspar_species(release = 2024, search = NULL, order = NULL, ...) } \arguments{ -\item{release}{Numeric: (default = 2022) Which JASPAR database release -to use? Available options are: 2014, 2016, 2018, 2020, and 2022.} +\item{release}{Numeric: (default = 2024) Which JASPAR database release +to use? Available options are: 2024, 2022, 2020, 2018, 2016, and 2014.} \item{search}{Character: A search term.} @@ -30,30 +30,29 @@ JASPAR organizes matrix profiles from multiple species } \section{Corresponding API Resources}{ - "GET "https://jaspar.genereg.net/api/v1/species/" + "GET "https://jaspar.elixir.no/api/v1/species/" } \examples{ \donttest{ -rba_jaspar_species(release = 2022) +rba_jaspar_species(release = 2024) } } \references{ \itemize{ - \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva - Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, - Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol - Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel - Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris - Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, - Anthony Mathelier, JASPAR 2022: the 9th release of the open-access - database of transcription factor binding profiles, Nucleic Acids - Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, - https://doi.org/10.1093/nar/gkab1113 + \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, + Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, + Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard + B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: + 20th anniversary of the open-access database of transcription factor + binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 + \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data + from any programming language. Bioinformatics, 2017, + doi: 10.1093/bioinformatics/btx804 \item - \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} - \item \href{https://jaspar.genereg.net/faq/}{Citations note + \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} + \item \href{https://jaspar.elixir.no/faq/}{Citations note on JASPAR website} } } diff --git a/man/rba_jaspar_species_matrices.Rd b/man/rba_jaspar_species_matrices.Rd index d4e7af4d..a1e45d7a 100644 --- a/man/rba_jaspar_species_matrices.Rd +++ b/man/rba_jaspar_species_matrices.Rd @@ -6,7 +6,7 @@ \usage{ rba_jaspar_species_matrices( tax_id, - release = 2022, + release = 2024, only_last_version = FALSE, search = NULL, order = NULL, @@ -19,8 +19,8 @@ rba_jaspar_species_matrices( \item{tax_id}{Numeric: NCBI taxonomic Identifier of species. Use \code{\link{rba_jaspar_species}} to get a list of supported Species.} -\item{release}{Numeric: (default = 2022) Which JASPAR database release -to use? Available options are: 2014, 2016, 2018, 2020, and 2022.} +\item{release}{Numeric: (default = 2024) Which JASPAR database release +to use? Available options are: 2024, 2022, 2020, 2018, 2016, and 2014.} \item{only_last_version}{Logical: (default = FALSE) If TRUE, only the latest version of a matrix profile will be returned.} @@ -58,7 +58,7 @@ The results are paginated. You can control the page's size number } \section{Corresponding API Resources}{ - "GET "https://jaspar.genereg.net/api/v1/species/{tax_id}/" + "GET "https://jaspar.elixir.no/api/v1/species/{tax_id}/" } \examples{ @@ -69,19 +69,18 @@ rba_jaspar_species_matrices(tax_id = 9606, page_size = 100) } \references{ \itemize{ - \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva - Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, - Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol - Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel - Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris - Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, - Anthony Mathelier, JASPAR 2022: the 9th release of the open-access - database of transcription factor binding profiles, Nucleic Acids - Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, - https://doi.org/10.1093/nar/gkab1113 + \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, + Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, + Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard + B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: + 20th anniversary of the open-access database of transcription factor + binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 + \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data + from any programming language. Bioinformatics, 2017, + doi: 10.1093/bioinformatics/btx804 \item - \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} - \item \href{https://jaspar.genereg.net/faq/}{Citations note + \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} + \item \href{https://jaspar.elixir.no/faq/}{Citations note on JASPAR website} } } diff --git a/man/rba_jaspar_taxons.Rd b/man/rba_jaspar_taxons.Rd index 7236ac32..eda0535c 100644 --- a/man/rba_jaspar_taxons.Rd +++ b/man/rba_jaspar_taxons.Rd @@ -4,11 +4,11 @@ \alias{rba_jaspar_taxons} \title{List available taxonomic groups in JASPAR} \usage{ -rba_jaspar_taxons(release = 2022, ...) +rba_jaspar_taxons(release = 2024, ...) } \arguments{ -\item{release}{Numeric: (default = 2022) Which JASPAR database release -to use? Available options are: 2014, 2016, 2018, 2020, and 2022.} +\item{release}{Numeric: (default = 2024) Which JASPAR database release +to use? Available options are: 2024, 2022, 2020, 2018, 2016, and 2014.} \item{...}{rbioapi option(s). See \code{\link{rba_options}}'s arguments manual for more information on available options.} @@ -23,30 +23,29 @@ JASPAR organizes matrix profiles from multiple species } \section{Corresponding API Resources}{ - "GET "https://jaspar.genereg.net/api/v1/taxon/" + "GET "https://jaspar.elixir.no/api/v1/taxon/" } \examples{ \donttest{ -rba_jaspar_taxons(release = 2022) +rba_jaspar_taxons(release = 2024) } } \references{ \itemize{ - \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva - Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, - Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol - Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel - Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris - Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, - Anthony Mathelier, JASPAR 2022: the 9th release of the open-access - database of transcription factor binding profiles, Nucleic Acids - Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, - https://doi.org/10.1093/nar/gkab1113 + \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, + Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, + Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard + B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: + 20th anniversary of the open-access database of transcription factor + binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 + \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data + from any programming language. Bioinformatics, 2017, + doi: 10.1093/bioinformatics/btx804 \item - \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} - \item \href{https://jaspar.genereg.net/faq/}{Citations note + \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} + \item \href{https://jaspar.elixir.no/faq/}{Citations note on JASPAR website} } } diff --git a/man/rba_jaspar_taxons_matrices.Rd b/man/rba_jaspar_taxons_matrices.Rd index 27945c39..e974f86e 100644 --- a/man/rba_jaspar_taxons_matrices.Rd +++ b/man/rba_jaspar_taxons_matrices.Rd @@ -6,7 +6,7 @@ \usage{ rba_jaspar_taxons_matrices( tax_group, - release = 2022, + release = 2024, only_last_version = FALSE, search = NULL, order = NULL, @@ -20,8 +20,8 @@ rba_jaspar_taxons_matrices( \code{\link{rba_jaspar_taxons}} to get a list of supported Taxonomic groups.} -\item{release}{Numeric: (default = 2022) Which JASPAR database release -to use? Available options are: 2014, 2016, 2018, 2020, and 2022.} +\item{release}{Numeric: (default = 2024) Which JASPAR database release +to use? Available options are: 2024, 2022, 2020, 2018, 2016, and 2014.} \item{only_last_version}{Logical: (default = FALSE) If TRUE, only the latest version of a matrix profile will be returned.} @@ -60,7 +60,7 @@ The results are paginated. You can control the page's size number } \section{Corresponding API Resources}{ - "GET "https://jaspar.genereg.net/api/v1/taxon/{tax_group}/" + "GET "https://jaspar.elixir.no/api/v1/taxon/{tax_group}/" } \examples{ @@ -71,19 +71,18 @@ rba_jaspar_taxons_matrices(tax_group = "plants", page_size = 100) } \references{ \itemize{ - \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva - Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, - Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol - Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel - Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris - Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, - Anthony Mathelier, JASPAR 2022: the 9th release of the open-access - database of transcription factor binding profiles, Nucleic Acids - Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, - https://doi.org/10.1093/nar/gkab1113 + \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, + Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, + Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard + B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: + 20th anniversary of the open-access database of transcription factor + binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 + \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data + from any programming language. Bioinformatics, 2017, + doi: 10.1093/bioinformatics/btx804 \item - \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} - \item \href{https://jaspar.genereg.net/faq/}{Citations note + \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} + \item \href{https://jaspar.elixir.no/faq/}{Citations note on JASPAR website} } } diff --git a/man/rba_jaspar_tffm.Rd b/man/rba_jaspar_tffm.Rd index 83558d5b..97c14c78 100644 --- a/man/rba_jaspar_tffm.Rd +++ b/man/rba_jaspar_tffm.Rd @@ -23,7 +23,7 @@ Using this function you can retrieve details and annotations of } \section{Corresponding API Resources}{ - "GET "https://jaspar.genereg.net/api/v1/fttm/{tffm_id}/" + "GET "https://jaspar.elixir.no/api/v1/fttm/{tffm_id}/" } \examples{ @@ -34,19 +34,18 @@ rba_jaspar_tffm("TFFM0056.3") } \references{ \itemize{ - \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva - Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, - Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol - Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel - Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris - Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, - Anthony Mathelier, JASPAR 2022: the 9th release of the open-access - database of transcription factor binding profiles, Nucleic Acids - Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, - https://doi.org/10.1093/nar/gkab1113 + \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, + Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, + Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard + B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: + 20th anniversary of the open-access database of transcription factor + binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 + \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data + from any programming language. Bioinformatics, 2017, + doi: 10.1093/bioinformatics/btx804 \item - \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} - \item \href{https://jaspar.genereg.net/faq/}{Citations note + \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} + \item \href{https://jaspar.elixir.no/faq/}{Citations note on JASPAR website} } } diff --git a/man/rba_jaspar_tffm_search.Rd b/man/rba_jaspar_tffm_search.Rd index 722e97f6..b416382a 100644 --- a/man/rba_jaspar_tffm_search.Rd +++ b/man/rba_jaspar_tffm_search.Rd @@ -6,7 +6,7 @@ \usage{ rba_jaspar_tffm_search( term = NULL, - release = 2022, + release = 2024, tax_group = NULL, search = NULL, order = NULL, @@ -18,8 +18,8 @@ rba_jaspar_tffm_search( \arguments{ \item{term}{Character: A search term.} -\item{release}{Numeric: (default = 2022) Which JASPAR database release -to use? Available options are: 2014, 2016, 2018, 2020, and 2022.} +\item{release}{Numeric: (default = 2024) Which JASPAR database release +to use? Available options are: 2024, 2022, 2020, 2018, 2016, and 2014.} \item{tax_group}{Character: Taxonomic group. Use \code{\link{rba_jaspar_taxons}} to get a list of supported Taxonomic @@ -62,7 +62,7 @@ Note that this is a search function. Thus, you are not required to fill } \section{Corresponding API Resources}{ - "GET "https://jaspar.genereg.net/api/v1/api/v1/tffm/" + "GET "https://jaspar.elixir.no/api/v1/api/v1/tffm/" } \examples{ @@ -75,19 +75,18 @@ rba_jaspar_tffm_search(page_size = 100) } \references{ \itemize{ - \item Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva - Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, - Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol - Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel - Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris - Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, - Anthony Mathelier, JASPAR 2022: the 9th release of the open-access - database of transcription factor binding profiles, Nucleic Acids - Research, Volume 50, Issue D1, 7 January 2022, Pages D165–D173, - https://doi.org/10.1093/nar/gkab1113 + \item Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, + Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, + Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard + B, Sandelin A, Wasserman WW, Parcy F, Mathelier A JASPAR 2024: + 20th anniversary of the open-access database of transcription factor + binding profiles Nucleic Acids Res. in_press; doi: 10.1093/nar/gkad1059 + \item Khan, A. and Mathelier, A. JASPAR RESTful API: accessing JASPAR data + from any programming language. Bioinformatics, 2017, + doi: 10.1093/bioinformatics/btx804 \item - \href{https://jaspar.genereg.net/api/v1/docs/}{JASPAR API Documentation} - \item \href{https://jaspar.genereg.net/faq/}{Citations note + \href{https://jaspar.elixir.no/api/v1/docs/}{JASPAR API Documentation} + \item \href{https://jaspar.elixir.no/faq/}{Citations note on JASPAR website} } } diff --git a/vignettes/rbioapi.Rmd b/vignettes/rbioapi.Rmd index e4ace619..867e46c1 100644 --- a/vignettes/rbioapi.Rmd +++ b/vignettes/rbioapi.Rmd @@ -48,7 +48,7 @@ rbioapi is dedicated to **Biological or Medical** databases and web services. Cu On CRAN (Stable) version: () 1. [Enrichr](https://maayanlab.cloud/Enrichr/ "Enrichr") ([rbioapi vignette article](rbioapi_enrichr.html "rbioapi & Enrichr vignette article")) ^(new)^ -2. [JASPAR](https://jaspar.genereg.net/ "JASPAR - A database of transcription factor binding profiles") ([rbioapi vignette article](rbioapi_jaspar.html "rbioapi & Enrichr vignette article")) ^(new)^ +2. [JASPAR](https://jaspar.elixir.no/ "JASPAR - A database of transcription factor binding profiles") ([rbioapi vignette article](rbioapi_jaspar.html "rbioapi & Enrichr vignette article")) ^(new)^ 3. [miEAA](https://ccb-compute2.cs.uni-saarland.de/mieaa2 "miRNA Enrichment Analysis and Annotation Tool (miEAA)") ([rbioapi vignette article](rbioapi_mieaa.html "rbioapi & miEAA vignette article")) 4. [PANTHER](https://www.pantherdb.org "Protein Analysis THrough Evolutionary Relationships (PANTHER)") ([rbioapi vignette article](rbioapi_panther.html "rbioapi & PANTHER vignette article")) 5. [Reactome](https://reactome.org/) ([rbioapi vignette article](rbioapi_reactome.html "rbioapi & Reactome vignette article")) @@ -216,7 +216,7 @@ rbioapi is an interface between you and other databases and services. Thus, if y - [How to cite Enrichr](rbioapi_enrichr.html#citations "How to cite Enrichr"). (See on [Enrichr website](https://maayanlab.cloud/Enrichr/help#terms)) -- [How to cite JASPAR](rbioapi_jaspar.html#citations "How to cite JASPAR"). (See on [JASPAR website](https://jaspar.genereg.net/faq/)) +- [How to cite JASPAR](rbioapi_jaspar.html#citations "How to cite JASPAR"). (See on [JASPAR website](https://jaspar.elixir.no/faq/)) - [How to cite miEAA](rbioapi_mieaa.html#citations "How to cite miEAA"). (See on [miEAA website](https://ccb-compute2.cs.uni-saarland.de/mieaa2)) diff --git a/vignettes/rbioapi_jaspar.Rmd b/vignettes/rbioapi_jaspar.Rmd index 3770756b..bde4c06f 100644 --- a/vignettes/rbioapi_jaspar.Rmd +++ b/vignettes/rbioapi_jaspar.Rmd @@ -39,7 +39,7 @@ rba_options(timeout = 30, skip_error = TRUE) Directly quoting from Fornes O, Castro-Mondragon JA, Khan A, et al: -> JASPAR ([https://jaspar.genereg.net)](https://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) for TFs across multiple species in six taxonomic groups. In this 8th release of JASPAR, the CORE collection has been expanded with 245 new PFMs (169 for vertebrates, 42 for plants, 17 for nematodes, 10 for insects, and 7 for fungi), and 156 PFMs were updated (125 for vertebrates, 28 for plants and 3 for insects). These new profiles represent an 18% expansion compared to the previous release. +> JASPAR ([https://jaspar.elixir.no)](https://jaspar.elixir.no) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) for TFs across multiple species in six taxonomic groups. In this 8th release of JASPAR, the CORE collection has been expanded with 245 new PFMs (169 for vertebrates, 42 for plants, 17 for nematodes, 10 for insects, and 7 for fungi), and 156 PFMs were updated (125 for vertebrates, 28 for plants and 3 for insects). These new profiles represent an 18% expansion compared to the previous release. > > source:\ > Fornes O, Castro-Mondragon JA, Khan A, et al. JASPAR 2020: update of the open-access database of transcription factor binding profiles. *Nucleic Acids Res*. 2019; doi: [10.1093/nar/gkz1001](https://doi.org/10.1093/nar/gkz1001) @@ -63,7 +63,7 @@ release_7_info <- rba_jaspar_releases(7) ### Collections {#collections .heading3} -Within a release, Matrix profiles are organized into collections, You can use `rba_jaspar_collections()` to get a list of available collections, or read "JASPAR Collections" section in [documentation page in JASPAR web-site](https://jaspar.genereg.net/docs/ "JASPAR Documentation") for a thorough review. +Within a release, Matrix profiles are organized into collections, You can use `rba_jaspar_collections()` to get a list of available collections, or read "JASPAR Collections" section in [documentation page in JASPAR web-site](https://jaspar.elixir.no/docs/ "JASPAR Documentation") for a thorough review. ```{r collections} ## To get a list of available collection in release 2020: @@ -225,9 +225,11 @@ str(TFFM0056) ## How to Cite? {#citations .heading2} -To cite JASPAR (Please see ): +To cite JASPAR (Please see ): + +- Rauluseviciute I, Riudavets-Puig R, Blanc-Mathieu R, Castro-Mondragon JA, Ferenc K, Kumar V, Lemma RB, Lucas J, Chèneby J, Baranasic D, Khan A, Fornes O, Gundersen S, Johansen M, Hovig E, Lenhard B, Sandelin A, Wasserman WW, Parcy F, Mathelier A *JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles* Nucleic Acids Res. in_press; +- Khan, A. and Mathelier, A. *JASPAR RESTful API: accessing JASPAR data from any programming language*. Bioinformatics, 2017, -- Jaime A Castro-Mondragon, Rafael Riudavets-Puig, Ieva Rauluseviciute, Roza Berhanu Lemma, Laura Turchi, Romain Blanc-Mathieu, Jeremy Lucas, Paul Boddie, Aziz Khan, Nicolás Manosalva Pérez, Oriol Fornes, Tiffany Y Leung, Alejandro Aguirre, Fayrouz Hammal, Daniel Schmelter, Damir Baranasic, Benoit Ballester, Albin Sandelin, Boris Lenhard, Klaas Vandepoele, Wyeth W Wasserman, François Parcy, Anthony Mathelier, JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles, *Nucleic Acids Research*, Volume 50, Issue D1, 7 January 2022, Pages D165--D173, To cite rbioapi: