{"repo":"epigen/genome_tracks","free":true,"listed":false,"github":"https://github.com/epigen/genome_tracks","clone":"git clone https://github.com/epigen/genome_tracks.git","description":"A Snakemake workflow and MrBiomics module for easy visualization of genome browser tracks of aligned BAM files (e.g., RNA-seq, ATAC-seq, scRNA-seq, ...) powered by the wrapper gtracks for the package pyGenomeTracks, and IGV-reports.","language":"Python","stars":57,"topics":["atac-seq","bioinformatics","pipeline","python","rna-seq","snakemake","visualization","workflow","biomedical-data-science","genomic-regions"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Genome Browser Track Visualization Workflow A Snakemake 8 workflow for easy visualization of genome browser tracks of aligned/mapped BAM files (e.g., RNA-seq, ATAC-seq, scRNA-seq, ...) powered by the wrapper gtracks for the package pyGenomeTracks and IGV-reports. [!NOTE] This workflow adheres to the module specifications of MrBiomics, an effort to augment research by modularizing (biomedical) data science. For more details, instructions, and modules check out the project's repository. ⭐️ Star and share modules you find valuable 📤 - help others discover them, and guide our future work! [!IMPORTANT] If you use this workflow in a publication, please don't forget to give credit to the authors by citing it using this DOI 10.5281/zenodo.10849097. 🖋️ Authors - Stephan Reichl - Christoph Bock 💿 Software This project wouldn't be possible without the following software and their dependencies: Software Reference (DOI) :---: :---: deeptools https://doi.org/10.1093/nar/gkw257 gtracks https://gitlab.com/salk-tm/gtracks igv-reports https://github.com/igvteam/igv-reports pygenometracks https://doi.org/10.1093/bioinformatics/btaa692 samtools https://doi.org/10.1093/bioinformatics/btp352 sinto https://github.com/timoast/sinto 🔬 Methods This is a template for the Methods section of a scientific publication and is intended to serve as a starting point. Only retain paragraphs relevant to your analysis. References [ref] to the respective publications are curated in the software table above. Ve","default_branch":null,"files":null,"tree":[],"storefront":"/r/epigen","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/epigen/genome_tracks/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}