NEWS.md

In ytakemon/GINIR: Genetic inteRaction and EssenTiality neTwork mApper

GRETTA 2.7.0

Bugs in get_GeneNameID were fixed.

GRETTA 2.6.1

Bugs in select_cell_lines() were fixed.

GRETTA 2.6.0

Bugs in select_cell_lines() were fixed.

GRETTA 2.5.1

GRETTA 2.5.0

Bugs in list_mutations() were fixed.

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.

GRETTA 2.3.0

GRETTA 2.2.0

GRETTA 2.1.0

plot_screen() now has new option to plot specific genes using the gene_list = argument. Please read ?plot_screen for more info.

GRETTA 2.0.0

Major bump. New function GI_screen_perms() has been added to perform permutation on GI screen results for p-value correction/

GRETTA 1.0.6

Minor patch to for Connibear lab requests

GRETTA 1.0.5

Minor patch to remove duplicates from common screens

GRETTA 1.0.4

Minor patch to fix typo

GRETTA 1.0.3

Minor patch to fix protein expression extraction.

GRETTA 1.0.2

Minor patch to fix typo.

GRETTA 1.0.1

Minor patch to ensure top/bottoms are selected when annotating.

GRETTA 1.0.0

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.

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()

GRETTA 0.99.0

• Pre-release for Bioconductor submission

GRETTA 0.6.0

• 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.

GRETTA 0.5.0

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

GRETTA 0.4.1

• Users can now custom name their output files in GI_screen() and coessential_map() with the output_filename = option.
• Technically I think this should be a minor version update, but it seemed too insignificant to go to v0.5.0.

GRETTA 0.4.0

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

GRETTA 0.3.2

• GINIR package name has now changed to GRETTA (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

GINIR 0.3.1

• The patch fixes a bug that occurred when NAs were found in dependency probability columns (#33)

GINIR 0.3.0

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

GINIR 0.2.0

• First stable release of GINIR
• Contains citable DOI generated by Zenodo
• Users can now refer to the README page for a full tutorial of the tool and most up to date news.

ytakemon/GINIR documentation built on Oct. 11, 2024, 6:06 a.m.