Bioinformatics

Bioinformatics is an interdisciplinary field that intersects with biology, computer science, mathematics and statistics. It concerns itself with the development and use of methods and software tools for collecting and analyzing biological data.

Repositories 3,035

Developer-Y / cs-video-courses

12.9k

List of Computer Science courses with video lectures.

computer-science algorithms systems databases machine-learning web-development security computer-architecture bioinformatics robotics embedded-systems database-systems programming-language computer-vision

Updated Feb 13, 2019

plotly / dash

8.4k

Analytical Web Apps for Python. No JavaScript Required.

dash plotly data-visualization data-science gui-framework flask react python finance bioinformatics technical-computing charting plotly-dash web-app productivity no-javascript modeling no-vba

Python Updated Mar 20, 2019 2 issues need help

google / deepvariant

1.6k

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA…

tensorflow deep-neural-network genomics science dna sequencing genome bioinformatics deep-learning ngs deepvariant machine-learning

Python Updated Mar 16, 2019

bioconda / bioconda-recipes

911

Conda recipes for the bioconda channel.

bioinformatics conda package-management

Shell Updated Mar 22, 2019 10 issues need help

seandavi / awesome-single-cell

826

List of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

rna-seq-data gene-expression scrna-seq-data bioinformatics awesome-list dimensionality-reduction cell-cycle atac-seq analysis cell-differentiation python clustering cell-populations gene-expression-profiles rna-seq-experiments cell-clusters analysis-pipeline data-integration data-visualization

Updated Mar 18, 2019

nextflow-io / nextflow

740

A DSL for data-driven computational pipelines

bioinformatics workflow-engine pipeline pipeline-framework nextflow cloud data-flow groovy sge slurm aws docker singularity hpc singularity-containers reproducible-science reproducible-research

Groovy Updated Mar 21, 2019 14 issues need help

danielecook / Awesome-Bioinformatics

658

A curated list of awesome Bioinformatics libraries and software.

bioinformatics

Updated Sep 26, 2018

lh3 / bwa

658

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

bioinformatics sequence-alignment genomics fm-index

C Updated Jan 23, 2019

broadinstitute / gatk

585

Official code repository for GATK versions 4 and up

genomics spark science dna ngs sequencing genome bioinformatics gatk

Java Updated Mar 22, 2019 9 issues need help

galaxyproject / galaxy

553

Data intensive science for everyone.

bioinformatics workflow genomics science sequencing ngs dna usegalaxy docker pipeline workflow-engine

Python Updated Mar 22, 2019 56 issues need help

dib-lab / khmer

553

In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more

dna k-mer python bloom-filter count-min-sketch graph-traversal bioinformatics

Python Updated Mar 22, 2019

hail-is / hail

499

Scalable genomic data analysis.

genetics vcf genomics spark gwas bioinformatics python scala

Scala Updated Mar 22, 2019 2 issues need help

lh3 / seqtk

497

Toolkit for processing sequences in FASTA/Q formats

bioinformatics sequence-analysis

C Updated Feb 28, 2019

lh3 / minimap2

492

A versatile pairwise aligner for genomic and spliced nucleotide sequences

bioinformatics sequence-alignment spliced-alignment genomics

C Updated Mar 4, 2019

OpenGene / fastp

476

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting...)

C++ Updated Mar 21, 2019

scipipe / scipipe

469

SciPipe is a library for writing scientific workflows (sometimes also called "pipelines") of shell commands that depe…

scientific-workflows bioinformatics-pipeline workflow go dataflow pipeline cheminformatics bioinformatics fbp

Go Updated Mar 21, 2019

ewels / MultiQC

461

Aggregate results from bioinformatics analyses across many samples into a single report.

bioinformatics analysis pypi bioconda multiqc python

Python Updated Mar 21, 2019

google / nucleus

433

Python and C++ code for reading and writing genomics data.

genomics tensorflow dna bioinformatics

Python Updated Mar 21, 2019

broadinstitute / cromwell

384

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to m…

workflow-execution workflow cloud hpc bioinformatics executor scala docker ga4gh containers wdl workflow-description-language cwl common-workflow-language application

Scala Updated Mar 22, 2019

plotly / react-plotly.js

366

A plotly.js React component from Plotly 📈

react plotly data-visualization d3 charting-library bioinformatics fintech

JavaScript Updated Feb 25, 2019

lh3 / bioawk

344

BWK awk modified for biological data

bioinformatics sequence-analysis

C Updated Jan 1, 2019

shenwei356 / csvtk

326

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

csv tsv cross-platform golang toolkit bioinformatics command-line tool

Go Updated Feb 12, 2019

theislab / scanpy

323

Single-Cell Analysis in Python. Scales to >1M cells.

machine-learning data-science visualize-data genetics transcriptomics bioinformatics

Python Updated Mar 22, 2019

torognes / vsearch

317

Versatile open-source tool for metagenomics

metabarcoding metagenomics chimera alignment clustering search bioinformatics fastq fasta sequence microbiome amplicon

C++ Updated Mar 22, 2019

nicgirault / circosJS

314

d3 library to build circular graphs

d3js circos circos-graphs javascript circular bioinformatics bioinformatics-data big-data bigdata

JavaScript Updated May 27, 2018 1 issue needs help

GMOD / jbrowse

304

A modern genome browser built with JavaScript and HTML5.

genomics genome-browser genome-annotation protein-annotation bioinformatics biology

JavaScript Updated Mar 22, 2019 18 issues need help

biojava / biojava

299

📖

🔬

☕️ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

bioinformatics java protein-structure genomics protein-sequences protein-modification sequence-alignment structure-alignment protein-data-bank pdb parser-library structural-bioinformatics

Java Updated Mar 8, 2019 11 issues need help

deeptools / deepTools

299

Tools to process and analyze deep sequencing data.

python bioinformatics genomics ngs rna-seq chip-seq

Python Updated Mar 6, 2019

biod / sambamba

299

Tools for working with SAM/BAM/CRAM data

sam bam bioinformatics

D Updated Mar 16, 2019 5 issues need help

shenwei356 / seqkit

285

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang

bioinformatics cross-platform fasta golang sequence toolkit fastq tool manipulation

Go Updated Feb 27, 2019

Learn about bioinformatics

Wikipedia: Wikipedia

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