Biosurfer for systematic tracking of regulatory mechanisms leading to protein isoform diversity

This Zenodo repository contains data used for running Biosurfer_analysis, a tool to surf the biological network, from genome to transcriptome to proteome and back to gain insights into human disease biology.Repository content:

biosurfer_gencode_toy_data.zip: is a small subset of the GENCODE version 38 files (GTF, transcript FASTA, and protein FASTA) for the purpose of trial run and testing Biosurfer scripts.

biosurfer_gencode_toy_output.zip: Biosurfer generated output files for the toy data. 

biosurfer_gencode_v42_data.zip: contains GENCODE version 42 (basic) files (GTF, transcript FASTA, and protein FASTA).

biosurfer_gencode_v42_output.zip: Biosurfer generated output files for GENCODE 42 input files.

biosurfer_wtc11_data.zip: contains karyotypically normal human stem cell line data (WTC11) file (GTF, transcript FASTA, and protein FASTA).

biosurfer_wtc11_output.zip: Biosurfer generated output files for WTC11 files.

APPRIS analysis.zip: Intermediate files (CSV) detailing the APPRIS isoforms information utilized in the associated manuscript.

biosurfer_mouse.zip: contains GENCODE Mouse version M35 (basic) files (GTF, transcript FASTA, and protein FASTA).

biosurfer_mouse_output.zip: Biosurfer generated output files for GENCODE M35 input files.