PolyASite v3.0: a multi-species atlas of polyadenylation sites inferred from single-cell RNA-sequencing data
Year: 2024
Type: article
Abstract: This repository contains a supplementary jupyter notebook and necessary dependencies for the paper "PolyASite v3.0: a multi-species atlas of polyadenylation sites inferred from single-cell RNA-sequencing data". This jupyter notebook was used for data analysis, preparation of the UCSC track hub files, .bed and .tsv files for the PolyASite website, and generation of main and supplementary figure panels for the paper. The inputs for the notebook are the results of running SCINPAS workflow on a big compendium of Homo Sapiens, Mus Musculus, and C. elegans 10X scRNA-seq data (explained in details in the paper). In addition, notebook requires multiple annotation and genome files from public repositories (see the links within the notebook). To run the notebook "Analysis-clean.ipynb", please create a conda environment from the deposited file "analysis_env.yaml" and further select it in your jupyter lab or jupyter notebook instance (name of the environment is "polyAsite_v3"): conda env create -f analysis_env.yaml In addition, please download the table with considered canonical poly(A) motifs "motif_info.csv" and put it to the same directory as jupyter notebook.
Institutions: SIB Swiss Institute of Bioinformatics, University of Basel
Language: English
Topic: RNA Research and Splicing
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W6911754774
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