All Categories → Data Processing → bioinformatics

Top 704 bioinformatics open source projects

poreCov

SARS-CoV-2 workflow for nanopore sequence data

✭ 34

Nextflow python shell r workflow bioinformatics nanopore basecalling artic sars-cov-2 nanopore-data

pymsfilereader

Thermo MSFileReader Python bindings

✭ 58

python Batchfile bioinformatics mass-spectrometry comtypes-library

scarf

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

contact map

Contact map analysis for biomolecules; based on MDTraj

✭ 27

python shell bioinformatics molecular-dynamics computational-biology biochemistry protein-protein-interaction protein-ligand-interactions

sshash

A compressed, associative, exact, and weighted dictionary for k-mers.

✭ 62

C++shell CMake hashing bioinformatics dictionary k-mer minimal-perfect-hash

ginkgo

Cloud-based single-cell copy-number variation analysis tool

✭ 42

PHP javascript r shell C++CSS bioinformatics sequencing single-cell-genomics

GLUE

Graph-linked unified embedding for single-cell multi-omics data integration

✭ 180

python r Jupyter Notebook bioinformatics deep-learning single-cell single-cell-multiomics

assembly improvement

Improve the quality of a denovo assembly by scaffolding and gap filling

✭ 46

perl bioinformatics research genomics pathogen sequencing next-generation-sequencing bioinformatics-pipeline global-health infectious-diseases

Bioinformatics-Algorithms

Important bioinformatics algorithms as well as other useful scripts

✭ 23

python bioinformatics algorithms

SplitThreader

Explore rearrangements and copy-number amplifications in a cancer genome

✭ 65

javascript PHP python CSS HTML r shell visualization bioinformatics genomics

bioportal web ui

A Rails application for biological ontologies

✭ 20

javascript ruby Haml HTML CSS SCSS open-source metadata bioinformatics annotation rdf semantic-web owl open-science obo ruby-on-rails bioportal ontology-repository

GeneticVariation.jl

Datastructures and algorithms for working with genetic variation

✭ 33

julia bioinformatics snps biology mutation polymorphism variation

chise.js

A web application to visualize and edit the pathway models represented by SBGN Process Description Notation

✭ 15

javascript editor bioinformatics biology systems-biology pathways network-visualization pathway-analysis sbgn

AIML-in-Medicine-club

Repository for "AI/MD in Medicine" club in clubhouse

✭ 42

machine-learning bioinformatics ai medical-imaging clubhouse medical-ai healthcare-ai

biograkn

BioGrakn Knowledge Graph

✭ 169

bioinformatics knowledge-graph knowledge-discovery biomedical biograkn

workshops

Bioconnector Workshops

✭ 24

r HTML CSS shell workshops bioinformatics tutorial

sdust

Symmetric DUST for finding low-complexity regions in DNA sequences

✭ 24

c objective c Makefile bioinformatics

dockstore

Our VM/Docker sharing infrastructure and management component

✭ 99

java wdl Nextflow Common Workflow Language scala shell docker workflow bioinformatics containers cwl dockstore

homerkit

Read HOMER motif analysis output in R.

✭ 13

r bioinformatics enrichment transcription-factors rstats

electrostatics.github.io

APBS & PDB2PQR - software for biomolecular electrostatics and solvation

✭ 24

python HTML bioinformatics chemistry hacktoberfest biophysics

ngs-preprocess

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

✭ 22

Nextflow Dockerfile workflow bioinformatics pipeline reproducible-research ngs reproducible-science pacbio illumina nanopack trimgalore ngs-preprocess bax2bam porechop pacbio-ccs

haslr

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

✭ 68

C++python c Makefile bioinformatics nanopore genomics pacbio genome-assembly long-reads hybrid-assembly

manhattan generator

Manhattan plot Generator

✭ 20

python bioinformatics genomics genetics plot

biocommons.seqrepo

non-redundant, compressed, journalled, file-based storage for biological sequences

✭ 30

python Makefile shell perl bioinformatics sequences

atacr

Analysing Capture Seq Count Data

✭ 14

r science data bioinformatics genomics analysis capture rnaseq atac-seq count-data

CUT-RUNTools-2.0

CUT&RUN and CUT&Tag data processing and analysis

✭ 36

shell r python c awk bioinformatics genomics single-cell chromatin tf tn5 epigenome cutntag cutnrun

BioBlender21

Blender plugin to process biological data and molecular work.

✭ 65

python C++bioinformatics blender biology blender-addon bioinformatics-tool bioblender

muscle

Multiple sequence alignment with top benchmark scores scalable to thousands of sequences. Generates replicate alignments, enabling assessment of downstream analyses such as trees and predicted structures.

✭ 82

C++c bioinformatics algorithms biology

find differential primers

Code for design of diagnostic PCR primers, and metabarcoding markers.

✭ 46

python shell bioinformatics diagnostics qpcr bioinformatics-scripts primer-design diagnostic-primers

psamm

Curation and analysis of metabolic models

✭ 32

python bioinformatics metabolic-models metabolic-network

mapping-iterative-assembler

Consensus calling (or "reference assisted assembly"), chiefly of ancient mitochondria

✭ 15

c C++objective c haskell shell bioinformatics genomics alignment contamination mitochondria consensus-calling

mokapot

Fast and flexible semi-supervised learning for peptide detection in Python

✭ 25

python Dockerfile machine-learning bioinformatics conda proteomics percolator peptide-detection

IMGTHLA

Github for files currently published in the IPD-IMGT/HLA FTP Directory hosted at the European Bioinformatics Institute

✭ 135

Parrot bioinformatics

ontobio

python library for working with ontologies and ontology associations

✭ 104

python Jupyter Notebook bioinformatics graph sparql rdf semantic-web ontology gene-ontology obo obofoundry ontology-tools

orchid

A novel management, annotation, and machine learning framework for analyzing cancer mutations

✭ 29

Jupyter Notebook python machine-learning bioinformatics cancer-genomics variant-annotations

cromshell

CLI for interacting with Cromwell servers

✭ 43

shell wdl cli workflow bioinformatics cromwell

sinto

Tools for single-cell data processing

✭ 74

python bioinformatics single-cell

bionode-ncbi

Node.js module for working with the NCBI API (aka e-utils).

✭ 66

javascript Dockerfile nodejs bioinformatics tool api-client bionode

SigProfilerSimulator

SigProfilerSimulator allows realistic simulations of mutational patterns and mutational signatures in cancer genomes. The tool can be used to simulate signatures of single point mutations, double point mutations, and insertion/deletions. Further, the tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

✭ 18

python bioinformatics somatic-variants cancer-genomics mutational-signatures

GenAMap

Visual Machine Learning of Genome-Phenome Associations

✭ 22

C++javascript HTML CSS shell Starlark python bioinformatics gwas structured-association-mapping

DISCOVER

DISCOVER co-occurrence and mutual exclusivity analysis for cancer genomics data

✭ 21

fortran python r Makefile Batchfile shell bioinformatics genomics

nn-segmentation-for-lar

Neural networks to segment some type of biomedical images