Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
Projects in Awesome Lists tagged with bioinformatics
A curated list of projects in awesome lists tagged with bioinformatics .
https://github.com/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
Last synced: 29 Sep 2024
https://github.com/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
Last synced: 30 Jul 2024
https://github.com/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
Last synced: 29 Sep 2024
https://github.com/biopython/biopython
Official git repository for Biopython (originally converted from CVS)
bioinformatics biopython dna genomics phylogenetics protein protein-structure python sequence-alignment
Last synced: 29 Sep 2024
https://github.com/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
Last synced: 26 Sep 2024
https://github.com/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
Last synced: 30 Sep 2024
https://github.com/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
Last synced: 30 Sep 2024
https://github.com/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
Last synced: 03 Aug 2024
https://github.com/scverse/scanpy
Single-cell analysis in Python. Scales to >1M cells.
anndata bioinformatics data-science machine-learning python scanpy scverse transcriptomics visualize-data
Last synced: 01 Oct 2024
https://github.com/lh3/minimap2
A versatile pairwise aligner for genomic and spliced nucleotide sequences
bioinformatics genomics sequence-alignment spliced-alignment
Last synced: 01 Oct 2024
https://github.com/broadinstitute/gatk
Official code repository for GATK versions 4 and up
bioinformatics dna gatk genome genomics ngs science sequencing spark
Last synced: 28 Sep 2024
https://github.com/allenai/scispacy
A full spaCy pipeline and models for scientific/biomedical documents.
bioinformatics biomedical custom-pipes nlp scientific-documents spacy
Last synced: 30 Sep 2024
https://allenai.github.io/scispacy/
A full spaCy pipeline and models for scientific/biomedical documents.
bioinformatics biomedical custom-pipes nlp scientific-documents spacy
Last synced: 04 Aug 2024
https://github.com/bioconda/bioconda-recipes
Conda recipes for the bioconda channel.
bioinformatics conda hacktoberfest package-management
Last synced: 30 Sep 2024
https://github.com/lh3/bwa
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
bioinformatics fm-index genomics sequence-alignment
Last synced: 30 Sep 2024
https://github.com/soedinglab/mmseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
alignment bioinformatics blast linclust metagenomics mmseqs profile-search sequence-clustering sequence-search taxonomy
Last synced: 30 Sep 2024
https://github.com/soedinglab/MMseqs2
MMseqs2: ultra fast and sensitive search and clustering suite
alignment bioinformatics blast linclust metagenomics mmseqs profile-search sequence-clustering sequence-search taxonomy
Last synced: 02 Aug 2024
https://github.com/galaxyproject/galaxy
Data intensive science for everyone.
bioinformatics dna genomics hacktoberfest ngs pipeline science sequencing usegalaxy workflow workflow-engine
Last synced: 30 Sep 2024
https://github.com/lh3/seqtk
Toolkit for processing sequences in FASTA/Q formats
bioinformatics sequence-analysis
Last synced: 30 Sep 2024
https://github.com/shenwei356/seqkit
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
bioinformatics cross-platform fasta fastq golang manipulation sequence tool toolkit
Last synced: 02 Aug 2024
https://github.com/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
Last synced: 25 Sep 2024
https://github.com/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
Last synced: 02 Aug 2024
https://github.com/crazyhottommy/getting-started-with-genomics-tools-and-resources
Unix, R and python tools for genomics and data science
bioinformatics cancer-genomics data-science
Last synced: 30 Sep 2024
https://github.com/lightaime/deep_gcns_torch
Pytorch Repo for DeepGCNs (ICCV'2019 Oral, TPAMI'2021), DeeperGCN (arXiv'2020) and GNN1000(ICML'2021): https://www.deepgcns.org
3d-point-clouds bioinformatics cheminformatics computer-vision data-mining deep-gcns deep-learning geometric-deep-learning graph-convolutional-networks graph-neural-networks pytorch science-research social-network
Last synced: 30 Sep 2024
https://github.com/scipipe/scipipe
Robust, flexible and resource-efficient pipelines using Go and the commandline
bioinformatics bioinformatics-pipeline cheminformatics dataflow fbp go golang pipeline scientific-workflows scipipe workflow workflow-engine
Last synced: 01 Oct 2024
https://github.com/plotly/react-plotly.js
A plotly.js React component from Plotly đ
bioinformatics charting-library d3 data-visualization fintech plotly react
Last synced: 31 Jul 2024
https://github.com/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
Last synced: 02 Aug 2024
https://github.com/shenwei356/csvtk
A cross-platform, efficient and practical CSV/TSV toolkit in Golang
bioinformatics command-line cross-platform csv golang tool toolkit tsv
Last synced: 01 Aug 2024
https://github.com/broadinstitute/cromwell
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
application bioinformatics cloud containers docker executor ga4gh hpc scala wdl workflow workflow-description-language workflow-execution
Last synced: 31 Jul 2024
https://github.com/kexinhuang12345/DeepPurpose
A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)
bioinformatics covid19 ddi deep-learning drug-discovery drug-drug-interaction drug-property-prediction drug-repurposing drug-target-interaction drug-target-interactions dti-prediction ppi protein-function-prediction protein-protein-interaction qsar repurposing-drugs side-effects toolkit virtual-screening
Last synced: 01 Aug 2024
https://github.com/mims-harvard/TDC
Therapeutics Commons: Artificial Intelligence Foundation for Therapeutic Science
artificial-intelligence benchmarks bioinformatics biology biomedicine biotech cheminformatics chemistry datasets deep-learning drug-discovery machine-learning medicine precision-medicine therapeutics
Last synced: 01 Aug 2024
https://github.com/hail-is/hail
Cloud-native genomic dataframes and batch computing
bioinformatics genetics genomics gwas hail python software vcf
Last synced: 02 Aug 2024
https://github.com/kblin/ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
bioinformatics biology command-line download-genomes genbank genomics ncbi python
Last synced: 01 Aug 2024
https://github.com/scikit-bio/scikit-bio
scikit-bio: a community-driven Python library for bioinformatics, providing versatile data structures, algorithms and educational resources.
bioinformatics computational-biology
Last synced: 07 Aug 2024
https://github.com/shenwei356/rush
A cross-platform command-line tool for executing jobs in parallel
bioinformatics command cross-platform execute golang parallel pipeline shell windows
Last synced: 01 Aug 2024
https://github.com/google/nucleus
Python and C++ code for reading and writing genomics data.
bioinformatics dna genomics tensorflow
Last synced: 26 Sep 2024
https://github.com/samtools/htslib
C library for high-throughput sequencing data formats
bam bcf bioinformatics cram htslib ngs sam vcf
Last synced: 03 Aug 2024
https://github.com/tanghaibao/jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
allmaps assembly bioinformatics blast comparative-genomics genetic-maps genome-sequencing genomics sequence-alignments synteny variant-calling
Last synced: 29 Sep 2024
https://github.com/openwdl/wdl
Workflow Description Language - Specification and Implementations
bioinformatics cloud cromwell openwdl reproducibility reproducible-science wdl workflow
Last synced: 01 Aug 2024
https://github.com/COMBINE-lab/salmon
đ đŁ đą Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
10x bioinformatics c-plus-plus gene-expression quantification quasi-mapping rna-seq rna-seq-quantification rnaseq sailfish salmon scrna-seq selective-alignment single-cell single-cell-rna-seq transcriptome
Last synced: 03 Aug 2024
https://github.com/awslabs/dgl-lifesci
Python package for graph neural networks in chemistry and biology
bioinformatics cheminformatics deep-learning dgl drug-discovery geometric-deep-learning graph-neural-networks molecule
Last synced: 26 Sep 2024
https://github.com/biopandas/biopandas
Working with molecular structures in pandas DataFrames
bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure
Last synced: 26 Sep 2024
https://rasbt.github.io/biopandas
Working with molecular structures in pandas DataFrames
bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure
Last synced: 08 Sep 2024
https://github.com/BioPandas/biopandas
Working with molecular structures in pandas DataFrames
bioinformatics computational-biology drug-discovery mol2 molecular-structures molecule molecules pandas-dataframe pdb pdb-files protein-structure
Last synced: 06 Aug 2024
https://github.com/BioContainers/containers
Bioinformatics containers
biocontainers-architecture bioinformatics bioinformatics-analysis bioinformatics-containers docker-image dockerfiles rkt
Last synced: 02 Aug 2024
https://github.com/biocontainers/containers
Bioinformatics containers
biocontainers-architecture bioinformatics bioinformatics-analysis bioinformatics-containers docker-image dockerfiles rkt
Last synced: 28 Sep 2024
https://github.com/bebop/poly
A Go package for engineering organisms.
alignment bioengineering bioinformatics codon-optimizer computational-biology dna dna-barcode dna-barcoding fasta genbank genetic-engineering go golden-gate mash molecular-biology plasmids primer-design sequence-hashing synbio synthetic-biology
Last synced: 02 Aug 2024
https://github.com/deeptools/deepTools
Tools to process and analyze deep sequencing data.
bioinformatics chip-seq genomics ngs python rna-seq
Last synced: 02 Aug 2024
https://github.com/BenLangmead/bowtie2
A fast and sensitive gapped read aligner
bioinformatics c-plus-plus genomics read-aligners
Last synced: 02 Aug 2024
https://github.com/danforthcenter/plantcv
Plant phenotyping with image analysis
bioinformatics image-analysis plant-phenotyping plantcv science
Last synced: 31 Jul 2024
https://github.com/baranzinilab/kg_rag
Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks
bert-models bioinformatics bioinformatics-algorithms biomedical-applications biomedical-informatics context-aware gpt gpt35turbo gpt4 knowledge-base knowledge-graph large-language-models llama llama2 llm prompt-engineering prompt-tuning rag retrieval-augmented-generation sentence-transformers
Last synced: 27 Sep 2024
https://github.com/biotite-dev/biotite
A comprehensive library for computational molecular biology
bioinformatics computational-biology pdb-files sequence-analysis structural-biology
Last synced: 09 Aug 2024
https://github.com/ysig/GraKeL
A scikit-learn compatible library for graph kernels
bioinformatics chemoinformatics graph-classification graph-kernels graph-mining graph-similarity graph-similarity-algorithms scikit-learn
Last synced: 02 Aug 2024
https://github.com/lh3/bioawk
BWK awk modified for biological data
bioinformatics sequence-analysis
Last synced: 03 Aug 2024
https://github.com/plotly/dash-cytoscape
Interactive network visualization in Python and Dash, powered by Cytoscape.js
bioinformatics biopython computational-biology cytoscape cytoscapejs dash data-science graph-theory network-graph network-visualization plotly plotly-dash
Last synced: 01 Aug 2024
https://github.com/voutcn/megahit
Ultra-fast and memory-efficient (meta-)genome assembler
bioinformatics data-structures genome-assembly genomics metagenomics succinct
Last synced: 03 Aug 2024
https://github.com/BaranziniLab/KG_RAG
Empower Large Language Models (LLM) using Knowledge Graph based Retrieval-Augmented Generation (KG-RAG) for knowledge intensive tasks
bert-models bioinformatics bioinformatics-algorithms biomedical-applications biomedical-informatics context-aware gpt gpt35turbo gpt4 knowledge-base knowledge-graph large-language-models llama llama2 llm prompt-engineering prompt-tuning rag retrieval-augmented-generation sentence-transformers
Last synced: 31 Jul 2024
https://github.com/jts/nanopolish
Signal-level algorithms for MinION data
bioinformatics c-plus-plus epigenetics genome-assembly methylation science
Last synced: 02 Aug 2024
https://github.com/plotly/dash-bio
Open-source bioinformatics components for Dash
Last synced: 03 Aug 2024
https://github.com/soedinglab/hh-suite
Remote protein homology detection suite.
alignment bioinformatics cpp hh-suite hhblits hhpred hhsearch opensource profile-profile-search profile-search protein-structure sequence-search simd viterbi
Last synced: 03 Aug 2024
https://github.com/owkin/PyDESeq2
A Python implementation of the DESeq2 pipeline for bulk RNA-seq DEA.
bioinformatics differential-expression python rna-seq transcriptomics
Last synced: 03 Aug 2024
https://github.com/scverse/anndata
Annotated data.
anndata bioinformatics data-science machine-learning scanpy scverse transcriptomics
Last synced: 01 Aug 2024
https://github.com/nicgirault/circosJS
d3 library to build circular graphs
big-data bigdata bioinformatics bioinformatics-data circos circos-graphs circular d3js javascript
Last synced: 03 Aug 2024
https://github.com/nicgirault/circosjs
d3 library to build circular graphs
big-data bigdata bioinformatics bioinformatics-data circos circos-graphs circular d3js javascript
Last synced: 03 Oct 2024
https://github.com/insitro/redun
Yet another redundant workflow engine
aws bioinformatics data-engineering data-science docker etl gcp ml python workflow-engine
Last synced: 01 Aug 2024
https://github.com/plotly/dash.jl
Dash for Julia - A Julia interface to the Dash ecosystem for creating analytic web applications in Julia. No JavaScript required.
bioinformatics charting dash dashboard data-science data-visualization finance gui-framework julia modeling no-javascript no-vba plotly plotly-dash productivity react technical-computing web-app
Last synced: 29 Sep 2024
https://github.com/martinsos/edlib
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
alignment-path bioinformatics c-plus-plus edit-distance levehnstein-distance library python sequence-alignment
Last synced: 29 Sep 2024
https://github.com/Martinsos/edlib
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
alignment-path bioinformatics c-plus-plus edit-distance levehnstein-distance library python sequence-alignment
Last synced: 01 Aug 2024
https://github.com/cdk/cdk
The Chemistry Development Kit
bioinformatics blueobelisk cheminformatics chemistry code4lib java
Last synced: 02 Aug 2024
https://github.com/chhylp123/hifiasm
Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
bioinformatics denovo-assembly genomics hifi-read pacbio
Last synced: 02 Aug 2024
https://github.com/GMOD/jbrowse
JBrowse 1, a full-featured genome browser built with JavaScript and HTML5. For JBrowse 2, see https://github.com/GMOD/jbrowse-components.
bioinformatics biology genome-annotation genome-browser genomics protein-annotation
Last synced: 01 Aug 2024
https://github.com/mdshw5/pyfaidx
Efficient pythonic random access to fasta subsequences
bgzf bioinformatics dna fasta genomics indexing protein python samtools
Last synced: 02 Aug 2024
https://github.com/sourmash-bio/sourmash
Quickly search, compare, and analyze genomic and metagenomic data sets.
bioinformatics fracminhash hacktoberfest kmer minhash python rust scaled-minhash sketching sourmash taxonomic-classification taxonomic-profiling
Last synced: 08 Aug 2024
https://github.com/priyank-purohit/PostGUI
A React web application to query and share any PostgreSQL database.
admin bioinformatics dashboard data data-sharing database database-as-a-service database-gui genomics gui material-design material-ui postgres postgresql postgrest query-builder react react-admin reactjs typescript
Last synced: 08 Aug 2024
https://github.com/pharmai/plip
Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to đ Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294
bioinformatics docker openbabel pdb plip protein-structure python-bindings scientific-computing singularity
Last synced: 08 Aug 2024
https://github.com/oschwengers/bakta
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
annotation bacteria bacterial-genomes bioinformatics genome-annotation mag metagenome-assembled-genomes microbial-genomics plasmids
Last synced: 02 Oct 2024
https://github.com/openbiox/awosome-bioinformatics
A curated list of resources for learning bioinformatics.
bioinformatics data-analysis next-generation-sequencing
Last synced: 02 Aug 2024
https://github.com/adnanwahab/Simple-GPU
đŚ Functional WebGPU
bioinformatics data-science geospatial javascript regl robotics webgpu
Last synced: 03 Aug 2024
https://github.com/lh3/minigraph
Sequence-to-graph mapper and graph generator
bioinformatics genome-graph genomics pan-genome sequence-alignment
Last synced: 01 Aug 2024
https://github.com/aidenlab/juicer
A One-Click System for Analyzing Loop-Resolution Hi-C Experiments
3d-genome 3d-genome-browser bioinformatics genomics hi-c ngs
Last synced: 31 Jul 2024
https://github.com/Illumina/manta
Structural variant and indel caller for mapped sequencing data
bioinformatics indels structural-variation structural-variations
Last synced: 02 Aug 2024
https://github.com/seqan/seqan3
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
bioinformatics blast cpp-concepts cpp17 cpp20 fasta fastq fm-index modern samtools seqan sequence-alignment sequence-analysis
Last synced: 29 Sep 2024
https://github.com/FelixKrueger/Bismark
A tool to map bisulfite converted sequence reads and determine cytosine methylation states
bioinformatics dna methylation
Last synced: 01 Aug 2024
https://github.com/brentp/cyvcf2
cython + htslib == fast VCF and BCF processing
bioinformatics cython genomics htslib vcf
Last synced: 02 Aug 2024
https://github.com/bioconvert/bioconvert
Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.
bam2cram bam2sam bcf2vcf bigbed2bed bioinformatics conversion convertor cram2bam cram2sam embl2ena embl2fasta embl2genbank fasta2fastq genbank2embl genbank2fasta ngs phylogeny sam2bam sequence sniffer
Last synced: 03 Aug 2024
https://github.com/brentp/vcfanno
annotate a VCF with other VCFs/BEDs/tabixed files
annotation bioinformatics genomics vcf
Last synced: 02 Aug 2024
https://github.com/shenwei356/taxonkit
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
bioinformatics cross-platform lca lineage taxdump taxid taxonkit taxonomy
Last synced: 02 Aug 2024
https://github.com/Illumina/strelka
Strelka2 germline and somatic small variant caller
bioinformatics indels snps snvs
Last synced: 02 Aug 2024
https://github.com/gao-lab/GLUE
Graph-linked unified embedding for single-cell multi-omics data integration
bioinformatics deep-learning single-cell single-cell-multiomics
Last synced: 05 Aug 2024
https://github.com/mims-harvard/PrimeKG
Precision Medicine Knowledge Graph (PrimeKG)
bioinformatics dataset graph-machine-learning knowledge-graph network-medicine nlp-machine-learning precision-medicine therapeutics
Last synced: 02 Aug 2024
https://github.com/theislab/cellrank
CellRank: dynamics from multi-view single-cell data
bioinformatics cell-fate-determination cell-fate-transitions data-science fuzzy-clustering-analyses genetics machine-learning manifold-learning markov-chains rna-velocity single-cell-genomics single-cell-rna-seq trajectory-generation
Last synced: 02 Aug 2024
https://github.com/bionode/bionode
Modular and universal bioinformatics
bioinformatics bionode metapackage nodejs os4openscience tools
Last synced: 02 Aug 2024
https://github.com/tariqdaouda/pyGeno
Personalized Genomics and Proteomics. Main diet: Ensembl, side dishes: SNPs
bed bioinformatics biology cancer cancer-genomes cancer-genomics csv-parser ensembl genome genome-annotation genome-browser genome-sequencing genomes genomics gtf medical medicine proteomics snps vcf
Last synced: 01 Aug 2024
https://github.com/bcgsc/abyss
:microscope: Assemble large genomes using short reads
assembler bioinformatics bloom-filter c-plus-plus genome mpi openmp scaffold science
Last synced: 29 Sep 2024
https://github.com/lh3/miniprot
Align proteins to genomes with splicing and frameshift
bioinformatics sequence-alignment
Last synced: 03 Aug 2024
https://github.com/sanger-pathogens/Roary
Rapid large-scale prokaryote pan genome analysis
bioinformatics bioinformatics-pipeline genomics global-health infectious-diseases next-generation-sequencing pathogen research sequencing
Last synced: 01 Aug 2024
https://github.com/openbiox/weekly
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bioinformatics free-journals weekly
Last synced: 01 Aug 2024