Most popular bioinformatics repositories and open source projects

SNPRelate

R package: parallel computing toolset for relatedness and principal co...

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sinto

Tools for single-cell data processing

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CAFE5

Version 5 of the CAFE phylogenetics software

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biopython-coronavirus

Biopython Jupyter Notebook tutorial to characterize a small genome

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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...

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seqfu2

:rocket: seqfu - Sequece Fastx Utilities

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GenomicsDB

Highly performant data storage for importing, querying and transformin...

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flexidot

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

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scRNAseq_analysis_vignette

Tutorial for scRNA-seq data analysis beginners using R

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tftargets

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

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unimap

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

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pytabix

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

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SigProfilerMatrixGenerator

SigProfilerMatrixGenerator creates mutational matrices for all types o...

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pyhmmer

Cython bindings and Python interface to HMMER3.

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ilus

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

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Coursera-Specializations

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

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tasks

A collection of reusable WDL tasks. Category:Other

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plant-seg

A tool for cell instance aware segmentation in densely packed 3D volu...

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ntHash

Fast hash function for DNA sequences

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SnakeStrike

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

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BioBlender21

Blender plugin to process biological data and molecular work.

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fqgrep

Grep for FASTQ files

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oswitch

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

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GenomicDataCommons

Provide R access to the NCI Genomic Data Commons portal.

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BioStructures.jl

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

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pdb2pqr

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

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ProteinFlow

Versatile computational pipeline for processing protein structure data...

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fermi

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

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ohmnet

OhmNet: Representation learning in multi-layer graphs

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wgd

Python package and CLI for whole-genome duplication related analyses

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xpclr

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

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vcfpy

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

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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  

cwl-svg

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

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cmapR

Tools for manipulating annotated data matrices

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GEOquery

The bridge between the NCBI Gene Expression Omnibus and Bioconductor

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SemiBin

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bio

Bioinformatic infrastructure libraries

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haslr

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

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EDGE

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

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czid-web

Infectious Disease Sequencing Platform

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snps

tools for reading, writing, merging, and remapping SNPs

18   72   72  

pyrpipe

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

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pairix

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

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chaipcr

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

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Peptides

An R package to calculate indices and theoretical physicochemical prop...

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ANANSE

Prediction of key transcription factors in cell fate determination usi...

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DeepMicrobes

DeepMicrobes: taxonomic classification for metagenomics with deep lear...

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