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:
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.
Various code updates, new functions added for visualization, compatibility with modern R objects. Russell Bainer redesignated as official maintainer.
Miscellaneous minor report edits and performance upgrades. Bugfix to P-value based scoring algorithm. Peter Haverty designated as official maintainer.
First official release to Bioconductor.
Initial bioconductor submission.