Linux kernel source tree

A fast image processing library with low memory needs.

Locally run an Instruction-Tuned Chat-Style LLM

RNA-seq aligner

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Tools (written in C using htslib) for manipulating next-generation sequencing data

SRA Tools

The Levenshtein Python C extension module contains functions for fast computation of Levenshtein distance and string similarity

bedtools - the swiss army knife for genome arithmetic

C library for high-throughput sequencing data formats

Near-optimal RNA-Seq quantification

🔬 BEDOPS: high-performance genomic feature operations

Python package to read and write R RData and Rds files into/from pandas dataframes. No R or other external dependencies required.

A flexible framework for rapid genome analysis and interpretation

Short read de novo assembler using de Bruijn graphs, as published in: D.R. Zerbino and E. Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 1…

Reads simulator

A python extension for quick access to bigWig and bigBed files

Quadratic Programming Solver

miscellaneous scripts for bioinformatics/genomics that dont merit their own repo.

Basic operations on the space of numerical functions defined on the genome using lazy evaluators for flexibility and efficiency

Whole Genome Simulator for Next-Generation Sequencing

1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates

An illumina paired-end and mate-pair short read simulator. This project attempts to model as many of the quirks that exist in Illumina data as possible. Some of these quirks include the potential f…

De novo transcriptome assembler for short reads

Robust Allele Specific Quantification and quality controL

Rapid and robust analysis of RNA-Seq experiments.

ImReP is a computational method for rapid and accurate profiling of the adaptive immune repertoire from regular RNA-Seq data.

A Python interface to the BEDTools API using Cython

Hera-T, a fast and accurate tool for estimating gene abundances in single cell data generated by the 10X-Chromium protocol