bioinformatics

There are 1,676 repositories under bioinformatics topic.

Developer-Y / cs-video-courses
List of Computer Science courses with video lectures.
algorithms bioinformatics computational-biology computational-physics computer-architecture computer-science computer-vision database-systems databases deep-learning embedded-systems machine-learning quantum-computing reinforcement-learning robotics security systems web-development
66059
dash
plotly / dash
Data Apps & Dashboards for Python. No JavaScript Required.
bioinformatics charting dash data-science data-visualization finance flask gui-framework julia jupyter modeling plotly plotly-dash productivity python r react rstats technical-computing web-app
Language:Python 20927
biopython / biopython
Official git repository for Biopython (originally converted from CVS)
bioinformatics biopython dna genomics phylogenetics protein protein-structure python sequence-alignment
Language:Python 4244
google / deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
bioinformatics deep-learning deep-neural-network deepvariant dna genome genomics machine-learning ngs science sequencing tensorflow
Language:Python 3130
seandavi / awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
analysis analysis-pipeline atac-seq awesome-list bioinformatics cell-clusters cell-cycle cell-differentiation cell-populations clustering data-integration data-visualization dimensionality-reduction gene-expression gene-expression-profiles python rna-seq-data rna-seq-experiments scrna-seq-data single-cell
3021
danielecook / Awesome-Bioinformatics
A curated list of awesome Bioinformatics libraries and software.
awesome awesome-list bioinformatics
3003
nextflow
nextflow-io / nextflow
A DSL for data-driven computational pipelines
bioinformatics workflow-engine pipeline pipeline-framework nextflow cloud groovy sge slurm aws docker singularity hpc singularity-containers reproducible-science reproducible-research dataflow hello
Language:Groovy 2630
OpenGene / fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
adapter bioinformatics duplication fastq filter filtering illumina merging ngs overlap polyg preprocessing qc quality quality-control sequencing splitting trimming umi
Language:C++ 1832
scanpy
scverse / scanpy
Single-cell analysis in Python. Scales to >1M cells.
anndata bioinformatics data-science machine-learning python scanpy scverse transcriptomics visualize-data
Language:Python 1816
ColabFold
sokrypton / ColabFold
Making Protein folding accessible to all!
bioinformatics multiple-sequence-alignment protein-structure structure-prediction
Language:Jupyter Notebook 1812
lh3 / minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
bioinformatics genomics sequence-alignment spliced-alignment
Language:C 1731
scispacy
allenai / scispacy
A full spaCy pipeline and models for scientific/biomedical documents.
scientific-documents spacy custom-pipes nlp biomedical bioinformatics
Language:Python 1653
broadinstitute / gatk
Official code repository for GATK versions 4 and up
genomics spark science dna ngs sequencing genome bioinformatics gatk
Language:Java 1650
bioconda / bioconda-recipes
Conda recipes for the bioconda channel.
bioinformatics conda hacktoberfest package-management
Language:Shell 1599
lh3 / bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
bioinformatics sequence-alignment genomics fm-index
Language:C 1484
lh3 / seqtk
Toolkit for processing sequences in FASTA/Q formats
bioinformatics sequence-analysis
Language:C 1353
galaxyproject / galaxy
Data intensive science for everyone.
bioinformatics workflow genomics science sequencing ngs dna usegalaxy pipeline workflow-engine hacktoberfest
Language:Python 1348
MMseqs2
soedinglab / MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
alignment bioinformatics blast linclust metagenomics mmseqs profile-search sequence-clustering sequence-search taxonomy
Language:C 1319
shenwei356 / seqkit
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
bioinformatics cross-platform fasta fastq golang manipulation sequence tool toolkit
Language:Go 1250
MultiQC / MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
analysis bioconda bioinformatics data-visualization multiqc pypi python quality-control reporting seqera vizualisation
Language:JavaScript 1190
lightaime / deep_gcns_torch
Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org
graph-neural-networks geometric-deep-learning 3d-point-clouds deep-gcns data-mining pytorch computer-vision bioinformatics cheminformatics social-network science-research deep-learning graph-convolutional-networks
Language:Python 1132
crazyhottommy / getting-started-with-genomics-tools-and-resources
Unix, R and python tools for genomics and data science
bioinformatics cancer-genomics data-science
Language:Shell 1126
scipipe / scipipe
Robust, flexible and resource-efficient pipelines using Go and the commandline
scientific-workflows bioinformatics-pipeline workflow go dataflow pipeline cheminformatics bioinformatics fbp scipipe workflow-engine golang
Language:Go 1060
plotly / react-plotly.js
A plotly.js React component from Plotly 📈
react plotly data-visualization d3 charting-library bioinformatics fintech
Language:JavaScript 1004
graphein
a-r-j / graphein
Protein Graph Library
bioinformatics computational-biology deep-learning dgl drug-discovery gene-regulatory-networks geometric-deep-learning graph-neural-networks interactome interactomics ppi-networks protein protein-data-bank protein-design protein-structure python pytorch pytorch-geometric rna structural-biology
Language:Jupyter Notebook 1003
shenwei356 / csvtk
A cross-platform, efficient and practical CSV/TSV toolkit in Golang
bioinformatics command-line cross-platform csv golang tool toolkit tsv
Language:Go 985
cromwell
broadinstitute / cromwell
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
workflow-execution workflow cloud hpc bioinformatics executor scala docker ga4gh containers wdl workflow-description-language application
Language:Scala 975
bigdatagenomics / adam
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
avro big-data bioinformatics genomics java parquet python r scala spark
Language:Scala 968
mims-harvard / TDC
Therapeutics Commons: Artificial Intelligence Foundation for Therapeutic Science
machine-learning therapeutics drug-discovery datasets biology chemistry biomedicine bioinformatics cheminformatics deep-learning benchmarks artificial-intelligence precision-medicine medicine biotech
Language:Jupyter Notebook 963
hail
hail-is / hail
Cloud-native genomic dataframes and batch computing
genetics vcf genomics gwas bioinformatics python software hail
Language:Python 956
kexinhuang12345 / DeepPurpose
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
drug-repurposing deep-learning drug-target-interactions toolkit covid19 virtual-screening drug-discovery ppi ddi dti-prediction drug-property-prediction protein-function-prediction repurposing-drugs qsar side-effects drug-drug-interaction protein-protein-interaction drug-target-interaction bioinformatics
Language:Jupyter Notebook 939
kblin / ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
bioinformatics biology command-line download-genomes genbank genomics ncbi python
Language:Python 914
scikit-bio / scikit-bio
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
bioinformatics computational-biology
Language:Python 872
shenwei356 / rush
A cross-platform command-line tool for executing jobs in parallel
bioinformatics command cross-platform execute golang parallel pipeline shell windows
Language:Go 847
MareesAT / GWA_tutorial
A comprehensive tutorial about GWAS and PRS
gwas qc prs r plink genetics population-structure unix population-stratification genomics bioinformatics
791
samtools / htslib
C library for high-throughput sequencing data formats
htslib bioinformatics sam bam cram vcf bcf ngs
Language:C 788

Related Topics

genomics sequencing