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

<p>This Zenodo repository contains data used for running&nbsp;<a href="https://github.com/sheynkman-lab/biosurfer_analysis" target="_blank" rel="noopener">Biosurfer_analysis</a>, a tool to surf the biological network, from genome to transcriptome to proteome and back to gain insights into human disease biology.<br><br>Repository content:</p> <ol> <li><strong>biosurfer_gencode_toy_data.zip:</strong> 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.<br><br></li> <li><strong>biosurfer_gencode_toy_output.zip:&nbsp;</strong>Biosurfer generated output files for the toy data.&nbsp;<br><br></li> <li><strong>biosurfer_gencode_v42_data.zip:&nbsp;</strong>contains GENCODE version 42 (basic) files (GTF, transcript FASTA, and protein FASTA).<br><br></li> <li><strong>biosurfer_gencode_v42_output.zip: </strong>Biosurfer generated output files for GENCODE 42 input files.<br><br></li> <li><strong>biosurfer_wtc11_data.zip: </strong>contains karyotypically normal human stem cell line data (WTC11) file (GTF, transcript FASTA, and protein FASTA).<br><strong><br></strong></li> <li><strong>biosurfer_wtc11_output.zip:&nbsp;</strong>Biosurfer generated output files for WTC11 files.<br><br></li> <li><strong>APPRIS analysis.zip:&nbsp;</strong>Intermediate files (CSV) detailing the APPRIS isoforms information utilized in the associated manuscript.</li> <li><strong>biosurfer_mouse.zip: </strong>contains GENCODE Mouse version M35 (basic) files (GTF, transcript FASTA, and protein FASTA).</li> <li><strong>biosurfer_mouse_output.zip: </strong>Biosurfer generated output files for GENCODE M35 input files.</li> </ol>