Releases: MoTrPAC/MotrpacRatTraining6mo
Releases · MoTrPAC/MotrpacRatTraining6mo
It depends
Summer bug
Ready for the World
This package provides functions to fetch, explore, and reproduce the processed data and downstream analysis results presented in the main paper for the first large-scale multi-omic multi-tissue endurance exercise training study conducted in young adult rats by the Molecular Transducers of Physical Activity Consortium (MoTrPAC).
The goal of this release is to generate a citation in Zenodo
ATAC the bug
Summary:
- Bug fix in
atac_timewise_da()
andatac_training_da()
whenn_features = Inf
.
What's Changed
Full Changelog: v1.6.1...v1.6.2
Refmenable
Summary
- Accommodate RefMet IDs as feature IDs in
plot_feature_normalized_data()
andplot_feature_logfc()
. - Pass the user-supplied version of the feature identifier when
plot_feature_logfc()
is called withinplot_feature_normalized_data()
.
What's Changed
Full Changelog: v1.6.0...v1.6.1
Enriching
Summary
- Add functions for GSEA and PTM-SEA:
ssGSEA2_wrapper()
,prepare_gsea_input()
,
prepare_ptmsea_input()
,find_flanks()
,load_uniprot_human_fasta()
- Add
extract_top_trajectories()
function.
What's Changed
Full Changelog: v1.5.2...v1.6.0
He sed she sed
Summary
- For
enrichment_network_vis()
with argumentreturn_html=TRUE
, don't require GNU sed.
What's Changed
Full Changelog: v1.5.1...v1.5.2
Vizzy whiz
Summary
- In
enrichment_network_vis()
, include pathway names in determination of node labels. - In
enrichment_network_vis()
, useMotrpacRatTraining6moData::FEATURE_TO_GENE_FILT
as
feature_to_gene
default instead of the unfiltered version. - Add more details to
enrichment_network_vis()
docs.
What's Changed
Full Changelog: v1.5.0...v1.5.1
Major minor improvements
Summary
- Add
load_feature_annotation()
. MoTrPAC/MotrpacRatTraining6moData#43 - Add
tissues
,assays
, andcluster
arguments toenrichment_network_vis()
to
provide an alternate way for users to specify results fromMotrpacRatTraining6moData::GRAPH_PW_ENRICH
. - Add tests for
enrichment_network_vis()
. #45 - Use
signif()
instead ofround()
to display values in plot titles. #41 - Add
counts
argument totranscript_normalize_counts()
andatac_normalize_counts()
to allow user-supplied data. #43 - Add note about reproducibility issues to documentation for
transcript_normalize_counts()
. MoTrPAC/MotrpacRatTraining6moData#41 - Move
MotrpacRatTraining6moData
fromImports
toDepends
. This meansMotrpacRatTraining6moData
is also attached (not just loaded) whenMotrpacRatTraining6mo
is attached. #40 - Replace
fetch_object(name_as_string)
withget(name_as_string, envir=as.environment("package:MotrpacRatTraining6moData"))
. #40 - Change URLs for
load_methyl_feature_annotation()
andload_atac_feature_annotation()
. - Fix bug in
plot_feature_logfc()
that prevented epigenetic features from being plotted. - Speed up
plot_feature_logfc()
for differential epigenetic features. - In
get_rdata_from_url()
, calculate log fold-change standard errors for METHYL
differential analysis results:logFC_se = logFC/zscore
MoTrPAC/MotrpacRatTraining6moData#44 - Require newest version of
MotrpacRatTraining6moData
.
What's Changed
Full Changelog: v1.4.3...v1.5.0
Try try again
Summary
- In
plot_feature_normalized_data()
andplot_feature_logfc()
, handle input features that don't exist in the data.
What's Changed
Full Changelog: v1.4.2...v1.4.3