NEWS.md

In RussBainer/gCrisprTools: Suite of Functions for Pooled Crispr Screen QC and Analysis

Version 0.99.0:

Initial bioconductor submission.

Version 1.0.0:

First official release to Bioconductor.

Version 1.1.0:

Miscellaneous minor report edits and performance upgrades. Bugfix to P-value based scoring algorithm. Peter Haverty designated as official maintainer.

Version 1.15.0:

Various code updates, new functions added for visualization, compatibility with modern R objects. Russell Bainer redesignated as official maintainer.

Version 1.20.0:

Inclusion of factored quantile normalization and additional convenience functions, typo revisions in the vignettes. Suppression of results dataframe reordering by ct.generateResults(). Implementation of alternative reagent:target assignment, useful for situations where reagents are known to target multiple valid targets.

Version 2.0.0:

MAJOR UPDATE Adding the Following Functionality: Format, Library, and Testing Improvements* o Enable processing of libraries with 1:many reagent:target assignments o Standardization and clarification of Annotation objects and symbol/identifier relationships o Implementation of factored quantile normalization for timecourse screens o Introduction of the simpleResult format and integration with associated functions o Conditional testing framework for quantifying and visualizing signal agreement between contrasts

• Transition to gene set enrichment testing via Sparrow

o Implement wrappers and provide recommendations fopr geneset enrichment testing in pooled screens o Implementation of GREAT-style pathway mapping for libraries with heterogenous target:gene mappings o Summarization tools for comparing enrichment signals across screens

• New Visualization and Interpretation Tools

o Signal Summary Barchart (Single or Multiple Contrasts) o Waterfall reagent/target/pathway visualization (Single Contrast) o Contrast comparison plots: - Concordance at the Top (CAT) - Probability Space scatter plots - UpSet plots with conditional overlap framework

RussBainer/gCrisprTools documentation built on Nov. 5, 2022, 2:35 p.m.