This package is part of the pipeline developed for Genialis platform for processing shRNA data.

The main function is doDE, which performs importing of all the necessary parameters (from the parameters file) and performs the differential expression, classification and outputs results in text files. In addition, there are makeLibrary function which takes in a list of shRNA, gene and sequences and converts it to a valid .fasta file. Function summaryTable will scrape alignment and trimming reports and produce a summary table.

There are two inputs to doDE. One is a path to expression files. Each expression file has rows of shRNA and one column. Column should be named as sample (without file extensions, e.g. SCR-time0 for SCR-time0.txt). Second input is a parameter file. Currently this is an .xlsx file, but this limitation could be lifted in the future.

The file holds tabs sample_key, contrasts, overall_contrasts and classification_parameters. See file in inst/extdata for further details.

A word on sample_key tab. The study design should have fixed columns sample and replicate. All other columns which describe your experiment will be used to construct a formula used in DESeq as 0 + ... + replicate where ... represents a group of samples from the same treatment (e.g. sample-1 would belong to a group t0_control). Please see tests on how to run the pipeline as well as which outputs are expected. Each function should be documented. If you find any issues, please do not hesitate to post in Issue tracker.