Bioinformatics | Ecosyste.ms: Awesome

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: 13 Mar 2025

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: 18 Mar 2025

https://github.com/plotly/dash

Data Apps & Dashboards for Python. No JavaScript Required.

bioinformatics charting dash data-science data-visualization finance flask gui-framework jupyter modeling plotly plotly-dash productivity python react rstats technical-computing web-app

Last synced: 15 Apr 2025

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: 18 Apr 2025

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: 09 Apr 2025

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: 09 Apr 2025

https://github.com/sokrypton/colabfold

Making Protein folding accessible to all!

bioinformatics multiple-sequence-alignment protein-structure structure-prediction

Last synced: 09 Apr 2025

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: 10 Apr 2025

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: 09 Apr 2025

https://github.com/sokrypton/ColabFold

Making Protein folding accessible to all!

bioinformatics multiple-sequence-alignment protein-structure structure-prediction

Last synced: 27 Mar 2025

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: 14 Nov 2024

https://github.com/lh3/minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

bioinformatics genomics sequence-alignment spliced-alignment

Last synced: 09 Apr 2025

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: 10 Apr 2025

https://github.com/bioconda/bioconda-recipes

Conda recipes for the bioconda channel.

bioinformatics conda hacktoberfest package-management

Last synced: 08 Apr 2025

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: 09 Apr 2025

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: 21 Nov 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: 10 Apr 2025

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: 10 Apr 2025

https://github.com/lh3/seqtk

Toolkit for processing sequences in FASTA/Q formats

bioinformatics sequence-analysis

Last synced: 11 Apr 2025

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: 13 Nov 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: 08 Apr 2025

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: 19 Apr 2025

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: 09 Apr 2025

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: 12 Apr 2025

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: 13 Nov 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: 09 Apr 2025

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: 08 Apr 2025

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: 14 Apr 2025

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: 30 Mar 2025

https://github.com/plotly/react-plotly.js

A plotly.js React component from Plotly 📈

bioinformatics charting-library d3 data-visualization fintech plotly react

Last synced: 12 Apr 2025

https://github.com/mims-harvard/TDC

Therapeutics Commons (TDC-2): Multimodal 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: 30 Mar 2025

https://github.com/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

Last synced: 08 Apr 2025

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: 03 Apr 2025

https://github.com/hail-is/hail

Cloud-native genomic dataframes and batch computing

bioinformatics genetics genomics gwas hail python software vcf

Last synced: 09 Apr 2025

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: 27 Mar 2025

https://github.com/steineggerlab/foldseek

Foldseek enables fast and sensitive comparisons of large structure sets.

alignments bioinformatics clustering protein-structure

Last synced: 09 Apr 2025

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: 30 Mar 2025

https://github.com/moshi4/pycirclize

Circular visualization in Python (Circos Plot, Chord Diagram, Radar Chart)

bioinformatics chord-diagram circos comparative-genomics data-visualization dataviz genomics genomics-visualization matplotlib microbial-genomics phylogenetic-trees python radar-chart visualization

Last synced: 13 Apr 2025

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: 27 Nov 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: 06 Apr 2025

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: 14 Apr 2025

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: 10 Apr 2025

https://github.com/google/nucleus

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

bioinformatics dna genomics tensorflow

Last synced: 20 Jan 2025

https://github.com/openwdl/wdl

Workflow Description Language - Specification and Implementations

bioinformatics cloud cromwell openwdl reproducibility reproducible-science wdl workflow

Last synced: 09 Apr 2025

https://github.com/samtools/htslib

C library for high-throughput sequencing data formats

bam bcf bioinformatics cram htslib ngs sam vcf

Last synced: 16 Nov 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: 14 Apr 2025

https://github.com/COMBINE-lab/salmon

🐟 🍣 🍱 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: 17 Nov 2024

https://github.com/deeptools/deepTools

Tools to process and analyze deep sequencing data.

bioinformatics chip-seq genomics ngs python rna-seq

Last synced: 19 Apr 2025

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: 01 Jan 2025

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: 08 Apr 2025

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: 25 Nov 2024

https://github.com/benlangmead/bowtie2

A fast and sensitive gapped read aligner

bioinformatics c-plus-plus genomics read-aligners

Last synced: 13 Apr 2025

https://github.com/BioContainers/containers

Bioinformatics containers

biocontainers-architecture bioinformatics bioinformatics-analysis bioinformatics-containers docker-image dockerfiles rkt

Last synced: 13 Nov 2024

https://github.com/biocontainers/containers

Bioinformatics containers

biocontainers-architecture bioinformatics bioinformatics-analysis bioinformatics-containers docker-image dockerfiles rkt

Last synced: 13 Apr 2025

https://github.com/danforthcenter/plantcv

Plant phenotyping with image analysis

bioinformatics image-analysis plant-phenotyping plantcv science

Last synced: 27 Mar 2025

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: 13 Nov 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: 24 Mar 2025

https://github.com/BenLangmead/bowtie2

A fast and sensitive gapped read aligner

bioinformatics c-plus-plus genomics read-aligners

Last synced: 13 Nov 2024

https://github.com/edinburgh-genome-foundry/dnafeaturesviewer

:eye: Python library to plot DNA sequence features (e.g. from Genbank files)

bioinformatics dna-visualization genbank molecular-biology synthetic-biology visualization

Last synced: 13 Apr 2025

https://github.com/lh3/bioawk

BWK awk modified for biological data

bioinformatics sequence-analysis

Last synced: 12 Apr 2025

https://github.com/biojava/biojava

:book::microscope::coffee: BioJava is an open-source project dedicated to providing a Java library for processing biological data.

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

Last synced: 23 Mar 2025

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: 12 Nov 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: 13 Apr 2025

https://github.com/biotite-dev/biotite

A comprehensive library for computational molecular biology

bioinformatics computational-biology pdb-files sequence-analysis structural-biology

Last synced: 29 Nov 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: 16 Nov 2024

https://github.com/fritzsedlazeck/sniffles

Structural variation caller using third generation sequencing

bioconda bioinformatics nanopore ngm-lr pacbio structural-variation structural-variations

Last synced: 12 Apr 2025

https://github.com/Starlitnightly/omicverse

A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.

bioinformatics bulk-rna-seq omics single-cell

Last synced: 16 Mar 2025

https://github.com/voutcn/megahit

Ultra-fast and memory-efficient (meta-)genome assembler

bioinformatics data-structures genome-assembly genomics metagenomics succinct

Last synced: 15 Nov 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: 03 Apr 2025

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: 14 Apr 2025

https://github.com/biod/sambamba

Tools for working with SAM/BAM data

bam bioinformatics sam

Last synced: 14 Nov 2024

https://github.com/gamcil/clinker

Gene cluster comparison figure generator

bioinformatics d3js python visualization

Last synced: 10 Apr 2025

https://github.com/jts/nanopolish

Signal-level algorithms for MinION data

bioinformatics c-plus-plus epigenetics genome-assembly methylation science

Last synced: 13 Nov 2024

https://github.com/marcelm/cutadapt

Cutadapt removes adapter sequences from sequencing reads

bioinformatics python

Last synced: 14 Apr 2025

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 Apr 2025

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: 10 Apr 2025

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: 30 Mar 2025

https://github.com/chhylp123/hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads

bioinformatics denovo-assembly genomics hifi-read pacbio

Last synced: 13 Nov 2024

https://github.com/plotly/dash-bio

Open-source bioinformatics components for Dash

bioinformatics biojs dash

Last synced: 15 Nov 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: 14 Nov 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: 09 Apr 2025

https://github.com/tseemann/snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

bacteria bioinformatics fastq-analysis genomics haploid indel-discovery snps variant-calling vcf

Last synced: 12 Apr 2025

https://github.com/scverse/anndata

Annotated data.

anndata bioinformatics data-science machine-learning scanpy scverse transcriptomics

Last synced: 07 Apr 2025

https://github.com/cdk/cdk

The Chemistry Development Kit

bioinformatics blueobelisk cheminformatics chemistry code4lib java

Last synced: 13 Nov 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: 13 Apr 2025

https://github.com/crazyhottommy/bioinformatics-one-liners

Bioinformatics one liners from Ming Tang

bash bioinformatics

Last synced: 05 Apr 2025

https://github.com/plotly/react-cytoscapejs

React component for Cytoscape.js network visualisations

bioinformatics network-graph react

Last synced: 08 Apr 2025

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: 28 Nov 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: 13 Apr 2025

https://github.com/mdshw5/pyfaidx

Efficient pythonic random access to fasta subsequences

bgzf bioinformatics dna fasta genomics indexing protein python samtools

Last synced: 10 Apr 2025

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: 30 Mar 2025

https://github.com/poisonalien/maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.

bioinformatics cancer-genome-atlas cancer-genomics genomics maf-files r tcga

Last synced: 11 Apr 2025

https://github.com/pharmai/plip

Protein-Ligand Interaction Profiler - Analyze and visualize non-covalent protein-ligand interactions in PDB files according to 📝 Adasme et al. (2021), https://doi.org/10.1093/nar/gkab294

bioinformatics docker openbabel pdb plip protein-structure python-bindings scientific-computing singularity