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R toolkit for the analysis of single-cell chromatin data

Community-provided extensions to Seurat

Conda recipes for the bioconda channel.

This library provides implementations of many algorithms and data structures that are useful for bioinformatics. All provided implementations are rigorously tested via continuous integration.

sparse linear algebra library for rust

An R package implementing the UMAP dimensionality reduction method.

Fishpond: differential transcript and gene expression with inferential replicates

An efficient index for the colored, compacted, de Bruijn graph

A curated list of bioinformatics bench-marking papers and resources.

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments

De Bruijn graphs in Rust

A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data

Rcpp bindings for NumPy files

RNA-seq aligner

R toolkit for single cell genomics

Single-Cell RNA-seq pseudo-aligner

Examples analyses using the single-cell RNA-seq data from mouse cell atlases