bioinformatics

There are 1,394 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 programming-language computer-vision quantum-computing
36127
dash
plotly / dash
Analytical Web Apps for Python, R, Julia, and Jupyter. 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 16511
biopython / biopython
Official git repository for Biopython (originally converted from CVS)
bioinformatics biopython dna genomics phylogenetics protein protein-structure python sequence-alignment
Language:Python 3118
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 2488
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
2101
danielecook / Awesome-Bioinformatics
A curated list of awesome Bioinformatics libraries and software.
awesome awesome-list bioinformatics
1935
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 1726
bioconda / bioconda-recipes
Conda recipes for the bioconda channel.
bioinformatics conda package-management hacktoberfest
Language:Shell 1388
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++ 1248
broadinstitute / gatk
Official code repository for GATK versions 4 and up
genomics spark science dna ngs sequencing genome bioinformatics gatk
Language:Java 1230
lh3 / minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
bioinformatics genomics sequence-alignment spliced-alignment
Language:C 1204
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 1184
scispacy
allenai / scispacy
A full spaCy pipeline and models for scientific/biomedical documents.
bioinformatics biomedical custom-pipes nlp scientific-documents spacy
Language:Python 1156
lh3 / bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
bioinformatics sequence-alignment genomics fm-index
Language:C 1129
lh3 / seqtk
Toolkit for processing sequences in FASTA/Q formats
bioinformatics sequence-analysis
Language:C 967
galaxyproject / galaxy
Data intensive science for everyone.
bioinformatics workflow genomics science sequencing ngs dna usegalaxy docker pipeline workflow-engine hacktoberfest
Language:Python 958
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 924
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
Language:Go 921
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
Language:Python 885
ewels / MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
bioinformatics analysis pypi bioconda multiqc python
Language:Python 848
shenwei356 / seqkit
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation in Golang
bioinformatics cross-platform fasta golang sequence toolkit fastq tool manipulation
Language:Go 838
plotly / react-plotly.js
A plotly.js React component from Plotly 📈
bioinformatics charting-library d3 data-visualization fintech plotly react
Language:JavaScript 827
hail
hail-is / hail
Scalable genomic data analysis.
genetics vcf genomics spark gwas bioinformatics python scala software hail
Language:Python 801
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 cwl common-workflow-language application
Language:Scala 800
crazyhottommy / getting-started-with-genomics-tools-and-resources
Unix, R and python tools for genomics and data science
cancer-genomics bioinformatics data-science
Language:Shell 748
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 727
google / nucleus
Python and C++ code for reading and writing genomics data.
bioinformatics dna genomics tensorflow
Language:C++ 703
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 683
dib-lab / khmer
In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more
dna k-mer python bloom-filter count-min-sketch graph-traversal bioinformatics
Language:Python 678
kblin / ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
ncbi bioinformatics download-genomes python biology genomics command-line genbank
Language:Python 637
samtools / htslib
C library for high-throughput sequencing data formats
htslib bioinformatics sam bam cram vcf bcf ngs
Language:C 621
mims-harvard / TDC
Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development
benchmarks bioinformatics biology biomedicine cheminformatics chemistry datasets deep-learning drug-discovery machine-learning therapeutics
Language:Jupyter Notebook 609
seq-lang / seq
A high-performance, Pythonic language for bioinformatics
bioinformatics compiler computational-biology domain-specific-language genomics programming-language python
Language:C++ 605
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 581
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 572
COMBINE-lab / salmon
🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
quasi-mapping bioinformatics rna-seq rnaseq salmon quantification sailfish c-plus-plus gene-expression scrna-seq single-cell 10x selective-alignment rna-seq-quantification single-cell-rna-seq transcriptome
Language:C++ 548

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