AutoSigGen

Notebooks used to generate signatures for the Gene Centric GEO Reverse search (GCGRS) Appyter, which consists of the following:

Signature Generation Pipeline:

• 0_h5_processing.ipynb : extraction of bulk RNA-seq data from ARCHS4
• 1_sample_labelling.ipynb : grouping, labelling, scoring of samples to generate GSM list
• 2_gsms2sig.ipynb : calculation of signatures using GSM list
• 3_appyter_format_processing.ipynb : aggregation of signature data for ease of appyter query
• 4_score_extraction.ipynb : extraction and processing of signature scores

Gene Set Library Creation for Enrichr:

• sig2gene_set_library.ipynb : creation of gene set library from signature data