GRETTA 2.4.0

• Latest DepMap dataset 23Q4 is now available. See https://github.com/ytakemon/GRETTA/tree/main/DepMap_data_versions/ for more details.
• list_mutations(), list_cancer_types(), extract_rna(), select_cell_lines(), and list_mutations() have been updated to accommodate different column names used in 23Q4.
• plot_screen() now has new option to plot specific genes using the gene_list = argument. Please read ?plot_screen for more info.
• Major bump. New function GI_screen_perms() has been added to perform permutation on GI screen results for p-value correction/

v1.0.0

Due to slow turn around by Bioconductor, it has been decided that GRETTA will not be uploaded to their repository.

Introducing new functions!

• protien_coexpress() to perform co-expression analysis for protein data.
• common_coefs_prot() to map the Pearson's coefficient between input proteins.
• common_coefs_rna() to map the Pearson's coefficient between input RNA.
• common_coefs_coess() to map the Pearson's coefficient between input co/anti-essential genes.

Previous updates

GRETTA 0.99.5

• anntate_coess() was renamed to anntate_df()
• coessential_map(), get_inflection_point(), and anntate_coess() can now handle multiple input genes.
• Introducing new functions!:
• common_coefs() to map the Pearson's coefficient between all input genes.
• rna_coexpress() to perform co-expression analysis for mRNA.

GRETTA 0.99.4

Fixing path for figures in README to pass bioconductor warnings

GRETTA 0.99.3

Untracked files unrelated to R package devel that caused errors in bioconductor checks.

GRETTA 0.99.2

Removed all instances of lab path to pass bioconductor pre-check.

GRETTA 0.99.1

Added smaller example data to pass bioconductor pre-check.
Example data is now loaded using download_example_data()

v0.99.0

• For Bioconductor submission.
• This version is the same as 0.6.0 except for the version number to comply with Bioconductor instructions.

v0.6.0

• Version 0.5.0 was submitted to Bioinformatics and version 0.6.0 addresses several reviewer comments (detailed below).
• GRETTA is now GRETTA (with two T's) due conflict with existing package on CRAN.
• Upon loading GRETTA into R, a welcome message is displayed to indicate package version and the latest DepMap data set that is available.
• Function arguments are now all lower case.
• GI_screen() has a new argument gene_list = to allow small-scale GI screens and reduce computational time.
• Default pan-cancer coessential_map() now uses pre-computed cor matrix to reduce computational time. This matrix is provided along with the DepMap data.
• A vignette is now available and in a Bioconductor format to prepare for submission (same as readme).
• Examples are now mostly run-able to comply with Bioconductor.

v0.5.0

• Default output file name from GI_screen() has been renamed.
• Singularity definition file and tutorial file have been included as a supplement.

v0.4.0 GRETA now compatible with multiple version of DepMap data!

• All GRETA functions are now compatible with multiple DepMap data versions (20Q1, 21Q4, and 22Q2)!
• An FAQ section is now available here.

GINIR is now GRETA

• GINIR package name has now changed to GRETA (Genetic inteRaction and EssenTially mApper)
• GINI_screen() is now GI_screen()
• Added a NEWS.md file to track changes to the package.
• Back filled log for previous releases

Bug fixed in `GINI_screen()`

The patch fixes a bug that occurred when NAs were found in dependency probability columns.

v0.3.0 minor updates

This minor feature improvement now shows cell line IDs while listing all available mutations using list_available_mutations().

First GINIR release! v0.2.0

This is the first stable release of GINIR (v0.2.0), which contains a citable DOI generated by Zenodo.

Users can refer to the README page for a full tutorial of the tool as well as for the most up-to-date news and updates.