bioinformatics

There are 1,654 repositories under bioinformatics topic.

Developer-Y / cs-video-courses
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 computer-vision quantum-computing computational-biology computational-physics deep-learning reinforcement-learning
65112
dash
plotly / dash
Data Apps & Dashboards 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 modeling r rstats jupyter julia
Language:Python 20586
biopython / biopython
Official git repository for Biopython (originally converted from CVS)
python bioinformatics genomics biopython protein protein-structure sequence-alignment phylogenetics dna
Language:Python 4182
google / deepvariant
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
tensorflow deep-neural-network genomics science dna sequencing genome bioinformatics deep-learning ngs deepvariant machine-learning
Language:Python 3084
seandavi / awesome-single-cell
Community-curated 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 single-cell
2931
danielecook / Awesome-Bioinformatics
A curated list of awesome Bioinformatics libraries and software.
awesome awesome-list bioinformatics
2912
nextflow
nextflow-io / nextflow
A DSL for data-driven computational pipelines
aws bioinformatics cloud dataflow docker groovy hello hpc nextflow pipeline pipeline-framework reproducible-research reproducible-science sge singularity singularity-containers slurm workflow-engine
Language:Groovy 2556
OpenGene / fastp
An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)
fastq qc preprocessing filtering adapter overlap quality trimming splitting quality-control filter ngs bioinformatics umi sequencing illumina polyg duplication merging
Language:C++ 1783
scanpy
scverse / scanpy
Single-cell analysis in Python. Scales to >1M cells.
machine-learning data-science visualize-data transcriptomics bioinformatics scanpy anndata python scverse
Language:Python 1769
lh3 / minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
bioinformatics sequence-alignment spliced-alignment genomics
Language:C 1694
scispacy
allenai / scispacy
A full spaCy pipeline and models for scientific/biomedical documents.
bioinformatics biomedical custom-pipes nlp scientific-documents spacy
Language:Python 1617
broadinstitute / gatk
Official code repository for GATK versions 4 and up
genomics spark science dna ngs sequencing genome bioinformatics gatk
Language:Java 1609
bioconda / bioconda-recipes
Conda recipes for the bioconda channel.
bioinformatics conda hacktoberfest package-management
Language:Shell 1565
lh3 / bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
bioinformatics fm-index genomics sequence-alignment
Language:C 1454
galaxyproject / galaxy
Data intensive science for everyone.
bioinformatics workflow genomics science sequencing ngs dna usegalaxy pipeline workflow-engine hacktoberfest
Language:Python 1319
lh3 / seqtk
Toolkit for processing sequences in FASTA/Q formats
bioinformatics sequence-analysis
Language:C 1316
MMseqs2
soedinglab / MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
bioinformatics sequence-clustering profile-search sequence-search linclust mmseqs metagenomics alignment blast taxonomy
Language:C 1265
shenwei356 / seqkit
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
bioinformatics cross-platform fasta golang sequence toolkit fastq tool manipulation
Language:Go 1208
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 1177
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 1119
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 1104
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 1052
plotly / react-plotly.js
A plotly.js React component from Plotly 📈
react plotly data-visualization d3 charting-library bioinformatics fintech
Language:JavaScript 993
graphein
a-r-j / graphein
Protein Graph Library
protein protein-structure deep-learning pytorch graph-neural-networks dgl computational-biology bioinformatics structural-biology protein-data-bank protein-design geometric-deep-learning pytorch-geometric python interactomics interactome rna ppi-networks gene-regulatory-networks drug-discovery
Language:Jupyter Notebook 987
bigdatagenomics / adam
ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
spark big-data bioinformatics genomics parquet avro scala java python r
Language:Scala 968
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 962
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 959
hail
hail-is / hail
Cloud-native genomic dataframes and batch computing
genetics vcf genomics gwas bioinformatics python software hail
Language:Python 938
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 933
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 921
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 893
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 841
shenwei356 / rush
A cross-platform command-line tool for executing jobs in parallel
parallel golang cross-platform bioinformatics pipeline execute shell command windows
Language:Go 831
google / nucleus
Python and C++ code for reading and writing genomics data.
bioinformatics dna genomics tensorflow
Language:C++ 776
samtools / htslib
C library for high-throughput sequencing data formats
htslib bioinformatics sam bam cram vcf bcf ngs
Language:C 775
MareesAT / GWA_tutorial
A comprehensive tutorial about GWAS and PRS
gwas qc prs r plink genetics population-structure unix population-stratification genomics bioinformatics
767

Related Topics

genomics sequencing