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Top 704 bioinformatics open source projects

argparse2tool

transparently build CWL and Galaxy XML tool definitions for any script that uses argparse

✭ 24

python Common Workflow Language HTML bioinformatics usegalaxy

picardmetrics

🚦 Run Picard on BAM files and collate 90 metrics into one file.

✭ 38

shell Makefile picard bam-files bioinformatics quality-control rna-seq

echolocatoR

Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.

✭ 13

r python bioinformatics gwas linkage-disequilibrium qtl variant-annotation colocalization finemap echoverse

SigProfilerExtractor

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGen…

✭ 86

python bioinformatics somatic-variants cancer-genomics mutation-analysis mutational-signatures

Introduction to the Unix Shell for biologists

✭ 16

Makefile bioinformatics oer

AMIDD

Introduction to Applied Mathematics and Informatics in Drug Discovery (AMIDD)

✭ 13

TeX CSS bioinformatics statistics teaching drug-discovery informatics applied-mathematics chemoinformatics computing

matam

Mapping-Assisted Targeted-Assembly for Metagenomics

✭ 18

python Jupyter Notebook C++bioinformatics metagenomics rrna

polyRAD

Genotype Calling with Uncertainty from Sequencing Data in Polyploids 🍌🍓🥔🍠🥝

✭ 16

r python C++bioinformatics hacktoberfest genotype-likelihoods genotyping-by-sequencing snp-genotyping rad-seq dna-sequencing rad-sequencing

MSFragger

Ultrafast, comprehensive peptide identification for mass spectrometry–based proteomics

✭ 43

HTML bioinformatics proteomics mass-spectrometry database-search

bistro

A library to build and execute typed scientific workflows

✭ 43

ocaml workflow bioinformatics pipeline computational-biology

calour

exploratory and interactive microbiome analyses based on heatmaps

✭ 22

python HTML bioinformatics heatmap jupyter-notebook microbiome exploratory

motifmatchr

Fast motif matching in R

✭ 25

C++r bioinformatics motif-discovery

pathway-mapper

PathwayMapper: An interactive and collaborative graphical curation tool for cancer pathways

✭ 47

typescript CSS javascript graphviz bioinformatics systems-biology tcga cancer-genomics pathways network-visualization pathway-analysis cancer-pathways

react-msa-viewer

React rerelease of MSAViewer

✭ 15

javascript HTML react bioinformatics viewer msa multiple-sequence-alignment

awesome-genetics

A curated list of awesome bioinformatics software.

✭ 60

bioinformatics genomics genetics health dna ancestry snpedia 23andme geneology consumer-dna-test

TypeTE

Genotyping of segregating mobile elements insertions

✭ 15

perl python shell bioinformatics vcf alu transposons transposable-elements genotype-likelihoods genotyping short-reads

block-aligner

SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.

✭ 58

Jupyter Notebook rust shell bioinformatics algorithms webassembly wasm simd alignment avx2

netSmooth

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

✭ 23

r bioinformatics genomics single-cell

crazydoc

Read DNA sequences from colourful Microsoft Word documents

✭ 18

python bioinformatics synthetic-biology molecular-biology dna-sequences computer-aided-design

epiviz

EpiViz is a scientific information visualization tool for genetic and epigenetic data, used to aid in the exploration and understanding of correlations between various genome features.

✭ 65

javascript HTML CSS python PHP actionscript visualization bioinformatics epiviz epigenetic-data

chromap

Fast alignment and preprocessing of chromatin profiles

✭ 93

C++c Roff Makefile bioinformatics genomics sequence-analysis chromatin-profiles

perbase

Per-base per-nucleotide depth analysis

✭ 46

rust bioinformatics cli-app

reg-gen

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

✭ 64

python c shell CSS awk r bioinformatics dnase-seq genomics ngs chip-seq atac-seq footprinting differential-peak-calling

geneview

Genomics data visualization in Python by using matplotlib.

✭ 38

python Makefile visualization bioinformatics data-visualization matplotlib plotting bioinformatics-tool genomics-data-visualization

BioKEEN

A computational library for learning and evaluating biological knowledge graph embeddings

✭ 41

Jupyter Notebook python machine-learning bioinformatics linked-data knowledge-graph-embeddings

flexidot

Highly customizable, ambiguity-aware dotplots for visual sequence analyses

✭ 73

python visualization bioinformatics biology longest-common-subsequence sequence-analysis dotplot repetitive-dna pairwise-comparisons

ccs

CCS: Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads)

✭ 79

machine-learning bioinformatics consensus pacbio variant-calling ccs

plasmidtron

Assembling the cause of phenotypes and genotypes from NGS data

✭ 27

python shell Dockerfile bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

GenomicDataCommons

Provide R access to the NCI Genomic Data Commons portal.

✭ 64

r data-science bioinformatics genomics cancer tcga api-client core-services bioconductor vignette nci

StackedDAE

Stacked Denoising AutoEncoder based on TensorFlow

✭ 23

python r bioinformatics deep-neural-networks tensorflow autoencoders single-cell-rna-seq

bio tools

Useful bioinformatic scripts

✭ 35

shell perl forth python Smarty r bioinformatics

SumStatsRehab

GWAS summary statistics files QC tool

✭ 19

python bioinformatics gwas data-preprocessing data-preparation summary-statistics data-prep gwas-pipeline bioinformatics-tool gwas-summary-statistics sumstats

ngstools

My own tools code for NGS data analysis (Next Generation Sequencing)

✭ 28

python r bioinformatics next-generation-sequencing

referenceseeker

Rapid determination of appropriate reference genomes.

✭ 65

python Nextflow shell TeX bioinformatics microbiology wgs mash ani refseq reference-genomes

full spectrum bioinformatics

An open-access bioinformatics text

✭ 26

Jupyter Notebook HTML python bioinformatics genomics biology

OpenGene.jl

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

✭ 60

julia bioinformatics ngs

adversarial-relation-classification

Unsupervised domain adaptation method for relation extraction

✭ 18

python nlp machine-learning natural-language-processing bioinformatics nlp-machine-learning relation-extraction biomedical-data-science

dna-sculpture

3D printed sculpture of a DNA molecule, showing my own genome

✭ 22

python raspberry-pi bioinformatics electronics

orfipy

Fast and flexible ORF finder

✭ 27

python shell bioinformatics dna protein orf-detection orf-finder codon-tables extract-orfs orf-search

bystro

Bystro genetic analysis (annotation, filtering, statistics)

✭ 31

perl shell Dockerfile bioinformatics genomics bioinformatics-pipeline bioinformatics-analysis bioinformatics-scripts bioinformatics-databases bioinformatics-algorithms genomics-search

CATT

An ultra-sensitive and precise tool for characterizing T cell CDR3 sequences in TCR-seq and RNA-seq data.

✭ 17

julia python javascript shell bioinformatics tcr tcr-repertoire bioinformatics-tool

biskit

A Python platform for Structural Bioinformatics

✭ 47

python prolog bioinformatics scientific biophysics

SVCollector

Method to optimally select samples for validation and resequencing

✭ 20

C++Makefile perl r shell bioinformatics ngs vcf ngstools structural-variation long-reads

mulled

Mulled - Automatized Containerized Software Repository

✭ 49

docker bioinformatics rkt mulled involucro

staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.

✭ 52

python bioinformatics genomics antimicrobial-resistance

companion

This repository has been archived, currently maintained version is at https://github.com/iii-companion/companion

✭ 21

lua groovy ruby Dockerfile shell perl Nextflow bioinformatics pipeline parasites annotation genomics genome

calN50

Compute N50/NG50 and auN/auNG

✭ 20

javascript bioinformatics genomics

mview

MView extracts and reformats the results of a sequence database search or multiple alignment.

✭ 23

perl Makefile bioinformatics fasta blast blast-search bioinformatics-tool clustal sequence-alignment-visualization

CENTIPEDE.tutorial

🐛 How to use CENTIPEDE to determine if a transcription factor is bound.

✭ 23

r bioinformatics enrichment tutorial dnase-seq transcription-factors rstats

awesome-small-molecule-ml

A curated list of resources for machine learning for small-molecule drug discovery

✭ 54

machine-learning awesome bioinformatics cheminformatics drug-discovery awesome-list

hotmap

WebGL Heatmap Viewer for Big Data and Bioinformatics

✭ 13

javascript CSS HTML shell charts webgl bioinformatics big-data dataviz heatmap data-visualization pixijs data-analysis

CAFE5

Version 5 of the CAFE phylogenetics software

✭ 53

C++python bioinformatics phylogenetics gene-family

CoNekT

CoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.

✭ 17

python javascript HTML CSS flask bioinformatics rna-seq expression bootstrap3 cytoscapejs

gene-oracle

Feature extraction algorithm for genomic data

✭ 13

python Nextflow shell Dockerfile machine-learning bioinformatics gene rna-seq deep-learning genetic-algorithm dataset

catch

A package for designing compact and comprehensive capture probe sets.

✭ 55

python science bioinformatics genomics genome ngs sequencing metagenomics dna viral covid-19

tftargets

🎯 Human transcription factor target genes.

✭ 77

r python shell data bioinformatics transcription-factors rstats

2017 2018-single-cell-RNA-sequencing-Workshop-UCD UCB UCSF

2017_2018 single cell RNA sequencing Workshop UCD_UCB_UCSF

✭ 31

HTML bioinformatics workshop-materials scrna

nPhase

Ploidy agnostic phasing pipeline and algorithm

✭ 18

python bioinformatics bioinformatics-pipeline phasing polyploid

atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

✭ 109

python TeX Nextflow Dockerfile Common Workflow Language shell bioinformatics ngs trimming

MetaOmGraph

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

✭ 30

java Makefile bioinformatics rna-seq exploratory-data-analysis transcriptomics mog cancer-data big-data-visualization

301-360 of 704 bioinformatics projects