Runs ATARiS on RNAi reagent-level data.

Runs ATARiS on RNAi reagent-level data.

Collapses replicate samples in a gct data file, based on a sample information file\nSupports CRISPR cell line naming

Removes reagents with low read counts in original DNA plasmid pool. Outputs a GCT file containing filtered reagent data and a GCT file containing the mean read count for each reagent in the original DNA plasmid pool.

Removes shRNAs with low read counts in original DNA plasmid pool. Outputs a GCT file containing filtered shRNA data and a GCT file containing the mean read count for each shRNA in the original DNA plasmid pool.

Matches Fluidigm fingerprint report to reference set of CCLE SNP6.0 array data.\nTakes old Fluidigm software report or new PED style report (saved as .csv).\nAlso backwards compatible with Sequenom reports (Combine 100k and...

Filters a gct file to keep a user-defined list of reagents, also filters out NaNs (optional)

Filters out samples not in keeplist file

Makes a .cls file and matching .gct file using a column from the sample info file (for mutations) or an external annotation file.

Normalizes shRNA or CRISPR guide scores across cell lines using ZMAD, PMAD, rank, Z scores, global z-scores, lowess or quantile - ignores NaNs