Remove samples in dataset (.gct), using a list of samples provided

Maps reagents in a gct data file to genes based on a mapping file.

Calculate the fold change of each sample in a gct file, based on the appropriate DNA reference value (present in a gct file of the same dimension).

Runs ATARiS on RNAi reagent-level data.

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.

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

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

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

Filters a gct file of perturbation data based on the copy number of each gene. Uses a per cell line thresholds in an uploaded file.

Normalizes screening data to a file of negative control identifiers