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DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
Container class to represent genomic locations and support genomic analysis
SenePy is a set of tools to score single-cells based on their expression of cell-specific senescence markers. Please see the following publication By Sanborn MA et al in Nature Communications (2025…
A curated list of awesome curated lists of awesome softwares and resources in bioinformatics and affiliated areas
Structural Variant Identification Method using Genome Assemblies
Genome-in-a-Bottle stratifications for major references
A Python package for handling and visualizing GWAS summary statistics. https://cloufield.github.io/gwaslab/
Tools to scrape publication metadata from pubmed, arxiv, medrxiv, biorxiv and chemrxiv.
A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.
Collection of scripts to aid the analysis of Smart-seq+5'. Scripts cannot be used out-of-the-box, but are supposed to aid the understanding of methods used.
Wally: Visualization of aligned sequencing reads and contigs
A tool for somatic structural variant calling using long reads
a rust implementation of the splici algorithm to build spliced/unspliced transcripts
An ensemble approach to accurately detect somatic mutations using SomaticSeq
A set of command line utilities based on Rust-Bio.
[WORK IN PROGRESS]: Pysam2 is a module for Python 3.6 or newer for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib v2 C-API, the same one that powers samtoo…
Effortless Pixi Project Management Integration in VSCode
Simple, unified interface to multiple Generative AI providers
Build contrasts for models defined with formulaic
Zotero plugin to automatically move attachments and link them