NEWS.md

In acidgenomics/r-depmapanalysis: DepMap Analysis Utilities

DepMapAnalysis 0.2.0 (2021-07-09)

Major changes

• Support for legacy DepMapAnalysis and Achilles objects have been dropped in favor of simply using GeneEffect object class.
• Reworked internal DepMap dataset metadata to use YAML instead of list.
• Added support for Codependencies class, which imports the top 100 co-dependencies for a gene from DepMap.
• Added support for plotGeneEffectVsExpression.

Minor changes

• Resaved example objects.
• Improved code coverage to check support for all legacy datasets.

DepMapAnalysis 0.1.1 (2021-06-21)

New functions

• plotTopGeneEffectPerGroup: Added a new plotting function that makes it easier to visualize gene effects (dependency scores) across a subset of cell lines, such as specific lineages (solid tumors, blood cancer, etc.).

Minor changes

• Ensuring legacy Achilles S4 class definition remains exported, to maintain better backward compatibility with objects saved prior to v0.1.0 release, where we switched to DepMapAnalysis object as the primary class for analysis of Broad Achilles data.
• plotGeneEffect: Added support for violin geom, and improved consistency of ggplot2, using a switch call internally.
• Reworked some imports from basejump dependency package.

DepMapAnalysis 0.1.0 (2021-06-09)

Major changes

• Initial release version suitable for use on Shiny Server.
• Reworked object approach to now use DepMapAnalysis for both CRISPR and RNAi gene effect datasets. Previously, these were classed as Achilles and DEMETER2, which is confusing. Now both CRISPR and RNAi experiments keep track of project source and scoring method more clearly.
• Simplifed internal code to improve consistency between import of gene effect and gene expression from CCLE.
• DepMap releases starting from 2020 are supported.

DepMapAnalysis 0.0.6 (2021-03-12)

Minor changes

• Updated basejump dependencies, and removed now unnecessary stringr import.

DepMapAnalysis 0.0.5 (2021-02-25)

Major changes

• Improved metadata support for some CCLE functions, returning as SummarizedExperiment instead of DataFrame, when possible.

DepMapAnalysis 0.0.4 (2021-02-10)

Major changes

• Added support for 21Q1, 20Q4 v2, and 20Q4 releases.
• Switched Achilles object to inherit from SummarizedExperiment instead of RangedSummarizedExperiment.
• Gene metadata now comes from NCBI FTP server.
• DEMETER2 class objects now support colData and rowData.

DepMapAnalysis 0.0.3 (2020-10-07)

Minor changes

• Achilles: Gene synonyms are now fetched automatically, based on the new makeGRangesFromEnsembl update in basejump.
• Simplified internal BiocFileCache handling, using new cacheURL function defined in pipette package.

DepMapAnalysis 0.0.2 (2020-10-02)

New functions

• plotGeneEffect: Plot effect of gene knockdown as a boxplot or density plot.

Major changes

• Achilles object now requires slotting of common essential genes from DepMap. These are now imported automatically in the main Achilles() call.

DepMapAnalysis 0.0.1 (2020-10-02)

Initial release.

acidgenomics/r-depmapanalysis documentation built on Jan. 16, 2024, 10:52 p.m.