Most popular bioinformatics repositories and open source projects

dammit

just annotate it, dammit!

25   82   82  

flowr

Robust and efficient workflows using a simple language agnostic approa...

10   82   82  

myvariant.info

MyVariant.info: A BioThings API for human variant annotations

30   82   82  

bio

A lightweight and high-performance bioinformatics package in Golang

9   82   82  

dgenies

Dotplot large Genomes in an Interactive, Efficient and Simple way

13   82   82  

sinto

Tools for single-cell data processing

18   82   82  

CAFE5

Version 5 of the CAFE phylogenetics software

21   82   82  

Coursera-Specializations

Solutions to assignments of Coursera Specializations - Deep learning,...

49   81   81  

biopython-coronavirus

Biopython Jupyter Notebook tutorial to characterize a small genome

17   81   81  

aioli

Framework for building fast genomics web tools with WebAssembly and We...

7   81   81  

MicrobiomeBestPracticeReview

Current Challenges and Best Practice Protocols for Microbiome Analysis...

33   81   81  

seqfu2

:rocket: seqfu - Sequece Fastx Utilities

4   81   81  

flexidot

Highly customizable, ambiguity-aware dotplots for visual sequence anal...

16   80   80  

scRNAseq_analysis_vignette

Tutorial for scRNA-seq data analysis beginners using R

31   80   80  

pyhmmer

Cython bindings and Python interface to HMMER3.

9   79   79  

tftargets

:dart: Human transcription factor target genes from 6 databases in con...

18   79   79  

unimap

A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference al...

5   79   79  

pytabix

:card_index: Retrieve data in genomic intervals with a Python interfac...

8   79   79  

SigProfilerMatrixGenerator

SigProfilerMatrixGenerator creates mutational matrices for all types o...

31   79   79  

cwl-svg

A library for generating an interactive SVG visualization of CWL workf...

18   78   78  

ilus

A handy variant calling pipeline generator for whole-genome sequencing...

25   78   78  

tasks

A collection of reusable WDL tasks. Category:Other

30   77   77  

ntHash

Fast hash function for DNA sequences

13   76   76  

SnakeStrike

A Low-cost Open-source High-speed Multi-camera Motion Capture System.

21   76   76  

BioBlender21

Blender plugin to process biological data and molecular work.

11   76   76  

fqgrep

Grep for FASTQ files

3   76   76  

pdb2pqr

PDB2PQR - determining titration states, adding missing atoms, and assi...

22   75   75  

ProteinFlow

Versatile computational pipeline for processing protein structure data...

2   75   75  

oswitch

Provides access to complex Bioinformatics software (even BioLinux!) in...

9   75   75  

GenomicDataCommons

Provide R access to the NCI Genomic Data Commons portal.

22   75   75  

BioStructures.jl

A Julia package to read, write and manipulate macromolecular structure...

19   75   75  

fermi

A WGS de novo assembler based on the FMD-index for large genomes

15   74   74  

ohmnet

OhmNet: Representation learning in multi-layer graphs

32   74   74  

wgd

Python package and CLI for whole-genome duplication related analyses

39   74   74  

xpclr

Code to compute the XP-CLR statistic to infer natural selection

24   74   74  

vcfpy

Python 3 library with good support for both reading and writing VCF

13   74   74  

Cell_BLAST

A BLAST-like toolkit for large-scale scRNA-seq data querying and annot...

10   74   74  

MSFragger

Ultrafast, comprehensive peptide identification for mass spectrometry–...

6   74   74  

cmapR

Tools for manipulating annotated data matrices

33   73   73  

GEOquery

The bridge between the NCBI Gene Expression Omnibus and Bioconductor

34   73   73  

SemiBin

9   73   73  

bio

Bioinformatic infrastructure libraries

15   72   72  

haslr

A fast tool for hybrid genome assembly of long and short reads

8   72   72  

EDGE

EDGE is a highly adaptable bioinformatics platform that allows laborat...

32   72   72  

czid-web

Infectious Disease Sequencing Platform

19   72   72  

snps

tools for reading, writing, merging, and remapping SNPs

18   72   72  

pyrpipe

Reproducible bioinformatics pipelines in python. Import any Unix tool/...

28   72   72  

pairix

1D/2D indexing and querying on bgzipped text file with a pair of genom...

12   71   71  

chaipcr

The software behind Chai's open-source Real-Time PCR instrument

32   71   71  

EBImage

:art: Image processing toolbox for R

28   71   71