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Top 704 bioinformatics open source projects

A comprehensive tutorial about GWAS and PRS

✭ 303

r bioinformatics unix genomics

Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.

✭ 298

python library bioinformatics

Modular and universal bioinformatics

✭ 294

javascript nodejs tools bioinformatics

Therapeutics Data Commons: Machine Learning Datasets and Tasks for Therapeutics

✭ 291

jupyter-notebook machine-learning bioinformatics datasets chemistry biology cheminformatics

The Chemistry Development Kit

✭ 283

java bioinformatics chemistry cheminformatics

Accurate sample inference from amplicon data with single nucleotide resolution

✭ 276

r bioinformatics

An open source platform for managing and analyzing biomedical big data

✭ 274

python go ruby docker aws cloud azure workflow bioinformatics cluster gcp genomics bigdata workflow-engine

An analysis and visualization platform for 'omics data

✭ 273

javascript python visualization bioinformatics science

Structural variant and indel caller for mapped sequencing data

✭ 271

COBRApy is a package for constraint-based modeling of metabolic networks.

✭ 267

python bioinformatics flux modeling

A high-performance, Pythonic language for bioinformatics

✭ 263

python compiler bioinformatics genomics

Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs

✭ 261

python bioinformatics genomics medical biology csv-parser vcf genome cancer-genomics

A React web application to query and share any PostgreSQL database.

✭ 260

javascript typescript react database reactjs postgresql material-design gui dashboard data admin postgres bioinformatics material-ui genomics query-builder react-admin database-gui

annotate a VCF with other VCFs/BEDs/tabixed files

✭ 259

go bioinformatics genomics annotation vcf

Dnafeaturesviewer

👁 Python library to plot DNA sequence features (e.g. from Genbank files)

✭ 259

python visualization bioinformatics

[DEPRECATED] Bioinformatics and Computational Biology Infrastructure for Julia

✭ 257

julia bioinformatics deprecated genomics biology dna

deepsignal-plant

Detecting methylation using signal-level features from Nanopore sequencing reads of plants

✭ 21

python bioinformatics pytorch methylation plant nanopore-sequencing

varsome-api-client-python

Example client programs for Saphetor's VarSome annotation API

✭ 21

python bioinformatics genomics genome-annotation scientists

Highly adaptable common interface for proteomics search and de novo engines

✭ 22

java HTML XSLT perl GDB bioinformatics proteomics protein-identification

streamformatics

Real-time species-typing visualisation for nanopore data.

✭ 13

javascript python HTML CSS shell nodejs bioinformatics nanopore bioinformatics-pipeline d3js minimap2 japsa

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

✭ 52

python Nextflow shell Common Workflow Language bioinformatics ngs microbiology bacteria wgs contigs plasmids

Aim to be the bioinformatics repository with more and newer packages

✭ 13

shell python bioinformatics packages repository archlinux

This library tackles the construction and efficient execution of computational chemistry workflows

✭ 35

python Jupyter Notebook shell science automation bioinformatics materials chemistry quantum-mechanics scientific-workflows

Classifies genes as an oncogene, tumor suppressor gene, or as a non-driver gene by using Random Forests

✭ 44

python shell bioinformatics random-forest cancer somatic-variants driver-genes

Converts Prokka GFF3 files to EMBL files for uploading annotated assemblies to EBI

✭ 27

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

A standard implementation conforming to the Global Alliance for Genomics and Health (GA4GH) Workflow Execution Service (WES) API specification and a web application for managing and executing those WES services.

✭ 17

workflow bioinformatics workflow-management-system ga4gh-wes

The uncompromising Snakemake code formatter

✭ 78

python Vim Script Makefile formatter fmt bioinformatics snakemake code black codeformatter

Sample search by metadata and features

✭ 27

python shell Makefile bioinformatics microbiome qiime biom

A D library for computational biology and bioinformatics

✭ 45

d Ragel bioinformatics sam bam

WebLogo 3: Sequence Logos redrawn

✭ 106

python HTML Parrot PostScript shell CSS Makefile bioinformatics weblogo sequence-logos

ImmuneDB - A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data

✭ 13

python bioinformatics database immunology

For live demo, see http://lh3lh3.users.sourceforge.net/bioseq.shtml

✭ 34

HTML javascript bioinformatics sequence-alignment

📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics

✭ 84

Dockerfile perl shell docker dockerfiles bioinformatics containers singularity

The Microbiome Interpretable Temporal Rule Engine

✭ 37

python HTML bioinformatics computational-biology statistical-analysis bayesian-inference microbiome

lexicon-mono-seq

DOM Text Based Multiple Sequence Alignment Library

✭ 15

javascript TeX bioinformatics biology ascii vanilla-javascript data-visualization javascript-library async-programming ascii-art alignment help-wanted animation-library sequence-alignment msa good-first-issue msa-viewer

A simplified pipeline for ctDNA sequencing data analysis

✭ 29

shell perl bioinformatics pipeline ngs ctdna liquid-biopsy

MMseqs2 app to run on your workstation or servers

✭ 16

javascript go Vue CSS Makefile shell electron docker bioinformatics vue docker-compose profile-search sequence-search mmseqs

Phylogenetic trees in Julia

✭ 15

julia bioinformatics phylogenetic-trees phylogenetics

The Ontology for Biomedical Investigations

✭ 49

python Makefile ruby bioinformatics semantic-web owl ontology obo obofoundry

GenomeAnalysisModule

Welcome to the website and github repository for the Genome Analysis Module. This website will guide the learning experience for trainees in the UBC MSc Genetic Counselling Training Program, as they embark on a journey to learn about analyzing genomes.

✭ 19

HTML shell bioinformatics workshop genomics genome ubc vancouver dnaseq genetic bwamem bcchr richmond evidence2innovation short-read dna-seq bc-children-hospital genetic-counselling

micca - MICrobial Community Analysis

✭ 19

python Dockerfile bioinformatics clustering metagenomics amplicon

De novo assembly based variant calling pipeline for Illumina short reads

✭ 98

TeX javascript perl Makefile shell bioinformatics genomics variant-calling denovo-assembly

BACNET is a Java based platform to develop website for multi-omics analysis

✭ 12

java website bioinformatics genomics data-visualization proteomics transcriptomics bacnet multi-omics listeria

RNAseq titration results

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

✭ 22

r shell python Dockerfile machine-learning bioinformatics analysis cancer gene-expression rnaseq microarray normalization supplement

antigen.garnish

No description or website provided.

✭ 34

r Dockerfile machine-learning bioinformatics immunology peptides immunoinformatics

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.

✭ 23

Jupyter Notebook python bioinformatics bioinformatics-pipeline contact-matrix hi-c hic 3d-genome 3c capture-c

awesome-bioinformatics-formats

Curated list of bioinformatics formats and publications

✭ 50

bioinformatics awesome-list bioinformatics-data formats

conda-env-builder

Build and maintain multiple custom conda environments all in once place.

✭ 18

scala shell bioinformatics conda bioinformatics-pipeline conda-environment

𝙋𝙝𝙮𝙡𝙤𝙜𝙚𝙣𝙚𝙩𝙞𝙘 𝘾𝙤𝙢𝙥𝙤𝙣𝙚𝙣𝙩 𝙂𝙧𝙖𝙥𝙝 ⸺ Haskell program and libraries for general phylogenetic graph search

✭ 20

haskell c C++python Makefile Dhall bioinformatics graph-algorithms phylogenetics comparative-genomics phylogenetic-networks comparative-linguistics string-alignment

Earl Grey: A fully automated TE curation and annotation pipeline

✭ 25

python shell r perl Dockerfile bioinformatics genomics genome-annotation genome-analysis transposable-elements te-annotations

No description or website provided.

✭ 25

python bioinformatics metagenomics assembly-binning

A fast 23andMe genome text file parser, now superseded by arv

✭ 64

python C++CMake Makefile shell bioinformatics snps genomics dna snpedia 23andme health-report

📊 Identify cell types and pathways affected by genetic risk loci.

✭ 26

C++python r shell Makefile bioinformatics risk-loci gene tissue gene-sets algorithm enrichment gwas

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

✭ 91

C++bioinformatics duplex ngs sequencing consensus duplication deduplication somatic deep-sequencing sequencing-error sequencing-noise duplex-sequencing

Project metadata manager for PEPs in Python

✭ 29

python Jupyter Notebook r shell metadata bioinformatics ngs pipeline-submission-engine metadata-management

Predict plasmids from uncorrected long read data

✭ 27

python TeX Dockerfile bioinformatics research nanopore genomics pathogen bioinformatics-pipeline pacbio global-health kmer oxford-nanopore plasmid infectious-diseases long-reads uncorrected plasmidfinder

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

✭ 34

Jupyter Notebook python shell machine-learning bioinformatics rna-seq computational-biology ontologies cell-type-classification single-cell-rna-seq cell-biology cell-type

clustergrammer2-notebooks

Examples using Clustergrammer2 to explore high-dimensional datasets.

✭ 35

Jupyter Notebook HTML bioinformatics binder jupyter notebook scrna-seq binder-ready

Molecular informatics toolkit with a comprehensive integration of bioinformatics and cheminformatics tools for drug discovery.

✭ 22

r bioinformatics cheminformatics fingerprint feature-extraction bioconductor drug-discovery protein-sequences molecular-descriptors

VirNet: A deep attention model for viral reads identification

✭ 26

Jupyter Notebook python bioinformatics deep-learning keras metagenomics lstm

241-300 of 704 bioinformatics projects