Bioinformatics | Ecosyste.ms: Awesome

https://github.com/LooseLab/readfish

CLI tool for flexible and fast adaptive sampling on ONT sequencers

adaptive-sampling bioinformatics genomics ont oxford-nanopore sequencing

Last synced: 13 Nov 2024

https://github.com/lh3/kmer-cnt

Code examples of fast and simple k-mer counters for tutorial purposes

bioinformatics genomics k-mer-counting

Last synced: 17 Nov 2024

https://github.com/lh3/cgranges

A C/C++ library for fast interval overlap queries (with a "bedtools coverage" example)

algorithm bioinformatics genomics

Last synced: 27 Dec 2024

https://github.com/steineggerlab/foldmason

Multiple Protein Structure Alignment at Scale with FoldMason

bioinformatics msa protein-structure

Last synced: 09 Apr 2025

https://github.com/snakemake/snakefmt

The uncompromising Snakemake code formatter

bioinformatics black code codeformatter fmt formatter python snakemake

Last synced: 10 Apr 2025

https://github.com/lightaime/sgas

SGAS: Sequential Greedy Architecture Search (CVPR'2020) https://www.deepgcns.org/auto/sgas

3d-point-clouds automl bioinformatics computer-vision deep-gcns geometric-deep-learning graph-neural-networks neural-architecture-search

Last synced: 20 Mar 2025

https://github.com/mlin/GenomicSQLite

Genomics Extension for SQLite

bioinformatics genomics sequencing sqlite sqlite3

Last synced: 19 Nov 2024

https://github.com/mlin/genomicsqlite

Genomics Extension for SQLite

bioinformatics genomics sequencing sqlite sqlite3

Last synced: 05 Apr 2025

https://github.com/DecodeGenetics/graphtyper

Population-scale genotyping using pangenome graphs

bioinformatics decode-genetics genetics genotype graph variants

Last synced: 16 Nov 2024

https://github.com/fjossinet/rnartist

With RNArtist, you construct a collection of RNA structures that can be gathered into RNA families, projects,...

bioinformatics java javafx-application kotlin rna rna-secondary-structure rna-structure

Last synced: 13 Apr 2025

https://github.com/GreenleafLab/chromVAR

chromatin Variability Across Regions (of the genome!)

atac-seq bioinformatics dnase-seq r

Last synced: 16 Nov 2024

https://github.com/lh3/psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

bioinformatics genomics population-genetics

Last synced: 17 Nov 2024

https://github.com/brentp/hts-nim

nim wrapper for htslib for parsing genomics data files

bioinformatics genomics high-throughput-sequencing htslib nim nim-lang

Last synced: 11 Mar 2025

https://github.com/althonos/pyrodigal

Cython bindings and Python interface to Prodigal, an ORF finder for genomes and metagenomes. Now with SIMD!

bioconda bioinformatics cython-wrapper gene-finding genome metagenomes orf-finder prodigal python python-interface python-library simd

Last synced: 08 Apr 2025

https://github.com/soedinglab/plass

sensitive and precise assembly of short sequencing reads

bioinformatics metagenomics metatranscriptomics opensource proteins proteomics sequence-assembler

Last synced: 04 Apr 2025

https://github.com/biojulia/biosequences.jl

Biological sequences for the julia language

bioinformatics biojulia biological-sequences biology

Last synced: 12 Apr 2025

https://github.com/opengene/mutscan

Detect and visualize target mutations by scanning FastQ files directly

bioinformatics cancer detection fastq mutation ngs somatic validation variant visualization

Last synced: 10 Apr 2025

https://github.com/MathCancer/PhysiCell

PhysiCell: Scientist end users should use latest release! Developers please fork the development branch and submit PRs to the dev branch. Thanks!

3d agent-based-modeling bioinformatics cancer-research cross-platform physicell simulation-framework simulation-modeling tissue-engineering

Last synced: 13 Apr 2025

https://github.com/steineggerlab/foldcomp

Compressing protein structures effectively with torsion angles

bioinformatics compression protein-structure

Last synced: 09 Apr 2025

https://github.com/OpenGene/MutScan

Detect and visualize target mutations by scanning FastQ files directly

bioinformatics cancer detection fastq mutation ngs somatic validation variant visualization

Last synced: 16 Nov 2024

https://github.com/FreshAirTonight/af2complex

Predicting direct protein-protein interactions with AlphaFold deep learning neural network models.

alphafold2 bioinformatics deep-learning protein-complexes protein-protein-docking protein-protein-interaction protein-structure-prediction

Last synced: 12 Nov 2024

https://github.com/vanheeringen-lab/seq2science

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

atac-seq bioinformatics bioinformatics-pipeline chip-seq fastq ngs pipeline reproducible-research rna-seq snakemake sra workflows

Last synced: 19 Dec 2024

https://github.com/ngless-toolkit/ngless

NGLess: NGS with less work

bioinformatics bioinformatics-pipeline bwa fastq fastq-format genomics haskell haskell-language metagenomics next-generation-sequencing ngs samtools science

Last synced: 05 Apr 2025

https://github.com/scverse/rapids_singlecell

Rapids_singlecell: A GPU-accelerated tool for scRNA analysis. Offers seamless scverse compatibility for efficient single-cell data processing and analysis.

anndata bioinformatics gpu scverse single-cell

Last synced: 12 Nov 2024

https://github.com/jdblischak/smk-simple-slurm

A simple Snakemake profile for Slurm without --cluster-config

bioinformatics slurm snakemake snakemake-profile

Last synced: 10 Jan 2025

https://github.com/lynnlangit/aws-for-bioinformatics

AWS for Bioinformatics Researchers

athena aws aws-batch awsbatch bioinformatics ec2 genomics nextflow sagemaker

Last synced: 19 Apr 2025

https://github.com/aspjt/pax_sapientica

🌿: ABM & GIS for philological, archaeological, and anthropological data.

abm agent-based-modeling agent-based-simulation archaeology bioinformatics civilization elevation genomics geographical-information-system geography gis historical-data map openstreetmap osm sfml simulation simulator siv3d terrain

Last synced: 05 Apr 2025

https://github.com/marianattestad/assemblytics

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.

assembly bioinformatics genomics

Last synced: 05 Apr 2025

https://github.com/aehrc/variantspark

machine learning for genomic variants

association-studies aws bioinformatics databricks emr genome gwas notebook random-forest variant-spark variantspark vcf

Last synced: 06 Apr 2025

https://github.com/mmagnus/rna-tools

🔧rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) used by RNA CASP, RNA PUZZLES, and me ;-) docs @ http://rna-tools.rtfd.io web @ http://rna-tools.online

bioinformatics pdb python rna rna-pdb rna-puzzle rna-structure rna-tools rosetta simrna

Last synced: 21 Nov 2024

https://github.com/lh3/bedtk

A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)

bioinformatics

Last synced: 19 Dec 2024

https://github.com/pirovc/genome_updater

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

bash bioinformatics database download genbank genome genomes genomics ncbi refseq sequence

Last synced: 11 Apr 2025

https://github.com/brentp/peddy

genotype :: ped correspondence check, ancestry check, sex check. directly, quickly on VCF

ancestry bioinformatics genomics genotype pedigree vcf

Last synced: 07 Apr 2025

https://github.com/gabaldonlab/redundans

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

assembled-contigs assembly bioinformatics closing contigs docker-image fasta gap genome-assembly genomics heterozygous mate-pairs paired-end pipeline polymorphic python scaffolding

Last synced: 19 Dec 2024

https://github.com/genular/simon-frontend

PANDORA :computer:

bioinformatics biomarkers clinical-data clustering data-integration data-mining data-science data-visualization drug-discovery genomic-data-analysis machine-learning microbiome pandora predictive-analytics systems-biology transcriptomics tsne umap unsupervised-machine-learning

Last synced: 23 Jan 2025

https://github.com/cbg-ethz/V-pipe

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

biohackcovid20 biohackeu20 biohackeu21 biohackeu22 bioinformatics bioinformatics-pipeline conda genomics hiv ngs sars-cov-2 sarscov2 sequencing snakemake virus

Last synced: 23 Mar 2025

https://github.com/cbg-ethz/v-pipe

V-pipe is a pipeline designed for analysing NGS data of short viral genomes

biohackcovid20 biohackeu20 biohackeu21 biohackeu22 bioinformatics bioinformatics-pipeline conda genomics hiv ngs sars-cov-2 sarscov2 sequencing snakemake virus

Last synced: 05 Apr 2025

https://github.com/daniel-liu-c0deb0t/block-aligner

SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.

algorithms alignment avx2 bioinformatics neon rust simd wasm webassembly

Last synced: 06 Apr 2025

https://github.com/shixiangwang/sigminer

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html

bayesian-nmf bioinformatics cancer-research cnv copynumber-signatures cosmic-signatures dbs easy-to-use indel mutational-signatures nmf nmf-extraction r sbs signature-extraction somatic-mutations somatic-variants visualization

Last synced: 06 Apr 2025

https://github.com/genular/pandora

PANDORA - Predictive Analytics aNd Data Oriented Research Applications :computer:

bioinformatics biomarkers clinical-data clustering data-integration data-mining data-science data-visualization drug-discovery genomic-data-analysis machine-learning microbiome pandora predictive-analytics systems-biology transcriptomics tsne umap unsupervised-machine-learning

Last synced: 03 Apr 2025

https://github.com/ShixiangWang/sigminer

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html

bayesian-nmf bioinformatics cancer-research cnv copynumber-signatures cosmic-signatures dbs easy-to-use indel mutational-signatures nmf nmf-extraction r sbs signature-extraction somatic-mutations somatic-variants visualization

Last synced: 04 Dec 2024

https://github.com/shujiahuang/ilus

A lightweight and handy variant calling pipeline generator for whole-genome sequencing (WGS) and whole exom sequencing data (WES) analysis by using GATK and Sentieon. 一个基于 GATK 和 Sentieon 的简易且全面的 WGS/WES 分析流程生成器.

bioinformatics bioinformatics-pipeline pipeline variant-calling whole-genome-sequencing workflow-management

Last synced: 12 Apr 2025

https://github.com/lgatto/msnbase

Base Classes and Functions for Mass Spectrometry and Proteomics

bioconductor bioinformatics mass-spectrometry proteomics proteomics-data r visualisation

Last synced: 14 Apr 2025

https://github.com/kanaverse/kana

Single cell analysis in the browser

bioinformatics cite-seq exploratory-data-analysis interactive-analysis interactive-visualizations rna-seq single-cell webassembly

Last synced: 27 Dec 2024

https://github.com/pybel/pybel

🌶️ An ecosystem in Python for working with the Biological Expression Language (BEL)

bioinformatics biological-expression-language bioregistry domain-specific-language networks networks-biology pybel systems-biology

Last synced: 29 Nov 2024

https://github.com/steineggerlab/metabuli

Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid.

bioinformatics k-mer metagenomics taxonomic-classification taxonomy

Last synced: 09 Apr 2025

https://github.com/biolink/ontobio

python library for working with ontologies and ontology associations

bioinformatics gene-ontology graph obo obofoundry ontology ontology-tools python rdf semantic-web sparql

Last synced: 08 Apr 2025

https://github.com/ebi-webcomponents/nightingale

Data visualisation web components for the life sciences.

biohackeu21 biohackeu22 bioinformatics visualization webcomponents

Last synced: 08 Apr 2025

https://github.com/lh3/ksw2

Global alignment and alignment extension

bioinformatics sequence-alignment

Last synced: 17 Nov 2024

https://github.com/sstadick/perbase

Per-base per-nucleotide depth analysis

bioinformatics cli-app rust

Last synced: 07 Apr 2025

https://github.com/globalbioticinteractions/globalbioticinteractions

Global Biotic Interactions provides access to existing species interaction datasets

biodiversity bioinformatics biology diet diseases ecoinformatics ecology eol etl-framework food-webs globi parasites pollinators species-interactions

Last synced: 14 Nov 2024

https://github.com/Daniel-Liu-c0deb0t/block-aligner

SIMD-accelerated library for computing global and X-drop affine gap penalty sequence-to-sequence or sequence-to-profile alignments using an adaptive block-based algorithm.

algorithms alignment avx2 bioinformatics neon rust simd wasm webassembly

Last synced: 19 Nov 2024

https://github.com/psy-fer/squigglekit

SquiggleKit: A toolkit for manipulating nanopore signal data

bioinformatics nanopore

Last synced: 13 Apr 2025

https://github.com/lgatto/MSnbase

Base Classes and Functions for Mass Spectrometry and Proteomics

bioconductor bioinformatics mass-spectrometry proteomics proteomics-data r visualisation

Last synced: 12 Nov 2024

https://github.com/timoast/sinto

Tools for single-cell data processing

bioinformatics single-cell

Last synced: 07 Apr 2025

https://github.com/tolkit/telomeric-identifier

Identify and find telomeres, or telomeric repeats in a genome.

bioinformatics genome repeats rust telomere telomeres telomeric

Last synced: 12 Apr 2025

https://github.com/baldassarrefe/graph-network-explainability

Explainability techniques for Graph Networks, applied to a synthetic dataset and an organic chemistry task. Code for the workshop paper "Explainability Techniques for Graph Convolutional Networks" (ICML19)

artificial-intelligence bioinformatics explainability graph-networks

Last synced: 18 Mar 2025

https://github.com/opengene/genefuse

Gene fusion detection and visualization

alk bioinformatics cancer cosmic eml4 fusion gene ret ros1

Last synced: 10 Apr 2025

https://github.com/adibvafa/codontransformer

CodonTransformer: The ultimate tool for codon optimization, optimizing DNA sequences for heterologous protein expression across 164 species.

bioinformatics biotechnology codon codon-optimization codon-optimizer computational-biology deep-learning gene-expression machine-learning synthetic-biology

Last synced: 12 Apr 2025

https://github.com/Psy-Fer/SquiggleKit

SquiggleKit: A toolkit for manipulating nanopore signal data

bioinformatics nanopore

Last synced: 13 Nov 2024

https://github.com/yuanx749/py-cdhit

A Python package for CD-HIT, clustering protein or nucleotide sequences.

bioinformatics package sequence-analysis tool

Last synced: 04 Apr 2025

https://github.com/jdidion/atropos

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

bioinformatics ngs python3 trimming

Last synced: 05 Apr 2025

https://github.com/opengene/gencore

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

bioinformatics consensus deduplication deep-sequencing duplex duplex-sequencing duplication ngs sequencing sequencing-error sequencing-noise somatic

Last synced: 10 Apr 2025

https://github.com/bio4j/bio4j

Bio4j abstract model and general entry point to the project

bio4j bio4j-titan bioinformatics database gene-ontology graph graph-data graph-database graph-databases graph-queries graph-schema java java-8 ncbi-taxonomy property-graph protein proteins titan uniprot uniref

Last synced: 10 Apr 2025

https://github.com/daniel-liu-c0deb0t/cute-nucleotides

Cute tricks for SIMD vectorized binary encoding and decoding of nucleotides, in Rust.

algorithms avx2 bioinformatics rust simd sse

Last synced: 13 Apr 2025

https://github.com/karchinlab/open-cravat

A modular annotation tool for genomic variants

annotation-tool bioinformatics bioinformatics-pipeline bioinformatics-tool genomic-data-analysis genomics javascript python python3 variant-analysis variant-annotation variant-annotations

Last synced: 06 Apr 2025

https://github.com/cslarsen/arv

A fast 23andMe DNA parser and inferrer for Python

23andme bioinformatics dna genome python snpedia snps

Last synced: 19 Dec 2024

https://github.com/molgenis/molgenis

MOLGENIS - for scientific data: management, exploration, integration and analysis.

biobank bioinformatics catalogue freemarker genetics java javascript lifescience molgenis

Last synced: 05 Apr 2025

https://github.com/opengene/fastv

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.

2019-ncov bioinformatics coronavirus covid covid-19 hcov meta-genomics microbial-sequences mngs ngs sars-cov-2 sequencing viral viral-infectious-diseases virus visualization

Last synced: 10 Apr 2025

https://github.com/lh3/yak

Yet another k-mer analyzer

bioinformatics k-mer

Last synced: 17 Nov 2024

https://github.com/OpenGene/GeneFuse

Gene fusion detection and visualization

alk bioinformatics cancer cosmic eml4 fusion gene ret ros1

Last synced: 16 Nov 2024

https://github.com/maayanlab/biojupies

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

bioinformatics cloud dcppc jupyter notebook pipeline rna-seq systems-biology

Last synced: 05 Apr 2025

https://github.com/althonos/pyhmmer

Cython bindings and Python interface to HMMER3.

bioinformatics cython-library hidden-markov-model hmmer hmmer3 python-bindings python-library sequence-analysis

Last synced: 20 Mar 2025

https://github.com/csbiology/biofsharp

Open source bioinformatics and computational biology toolbox written in F#.

amino-acids biocontainers bioinformatics bioinformatics-containers biology biostatistics dataprocessing datascience docker fsharp nucleotides sequence-analysis

Last synced: 05 Apr 2025

https://github.com/Nesvilab/philosopher

PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering

bioinformatics data-analysis go mass-spectrometry ms-data proteomics

Last synced: 19 Apr 2025

https://github.com/OpenGene/gencore

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

bioinformatics consensus deduplication deep-sequencing duplex duplex-sequencing duplication ngs sequencing sequencing-error sequencing-noise somatic

Last synced: 16 Nov 2024

https://github.com/bioinfomaticsCSU/deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads

bioinformatics epigenetics methylation nanopore-sequencing tensorflow

Last synced: 13 Nov 2024

https://github.com/OpenGene/fastv

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.

2019-ncov bioinformatics coronavirus covid covid-19 hcov meta-genomics microbial-sequences mngs ngs sars-cov-2 sequencing viral viral-infectious-diseases virus visualization

Last synced: 16 Nov 2024

https://github.com/labsquare/fastqt

FastQC port to Qt5: A quality control tool for high throughput sequence data.

bioinformatics fastq fastq-format gui qt5

Last synced: 15 Dec 2024

https://github.com/mdshw5/fastqp

Simple FASTQ quality assessment using Python

bioinformatics fastq kmer-distribution nucleotide-plot python sam

Last synced: 18 Nov 2024

https://github.com/telatin/seqfu2

:rocket: seqfu - Sequece Fastx Utilities

bioconda bioinformatics bioinformatics-tool fasta fastq genomics ngs sequencing

Last synced: 13 Nov 2024

https://github.com/rcedgar/usearch12

Open-source usearch

bioinformatics bioinformatics-algorithms computational-biology nucleotide-alignment protein-alignment protein-sequences search-algorithms

Last synced: 19 Apr 2025

https://github.com/lh3/fermikit

De novo assembly based variant calling pipeline for Illumina short reads

bioinformatics denovo-assembly genomics variant-calling

Last synced: 12 Mar 2025

https://github.com/owlcollab/owltools

OWLTools

api bioinformatics build-tool ontology owl-api web-ontology-language

Last synced: 02 Apr 2025

https://github.com/maxvalue/terpene-profile-parser-for-cannabis-strains

Parser and database to index the terpene profile of different strains of Cannabis from online databases

analysis aromatherapy bioinformatics biological-data biological-data-analysis cannabis cannabis-strains crawler data-science database health plants python python-3 scrapy terpene-profile terpenes web-crawler web-crawler-python web-crawling

Last synced: 17 Nov 2024

https://github.com/lh3/hickit

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

bioinformatics genomics hi-c

Last synced: 17 Nov 2024

https://github.com/ctskennerton/minced

Mining CRISPRs in Environmental Datasets

bioinformatics crispr

Last synced: 21 Mar 2025

https://github.com/andrew-hossack/dash-tools

DashTools - Plotly Dash Command Line Tools - Create, Run and Deploy Templated Python Apps from Terminal

bioinformatics charting command-line dash data-science data-visualization finance flask gui-framework heroku heroku-cli modeling plotly plotly-dash productivity python technical-computing template tools web-app

Last synced: 12 Apr 2025

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

Sequence Indexing and Search

bioinformatics chapel compressed-suffix-array compression fm-index indexing information-retrieval search

Last synced: 05 Apr 2025

https://github.com/mhahsler/rblast

Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package

bioconductor bioinformatics blast-search

Last synced: 12 Apr 2025

https://github.com/zhengxwen/snprelate

R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)

bioinformatics gds-format pca r simd snp

Last synced: 08 Apr 2025

https://github.com/robertaboukhalil/fastq.bio

An interactive web tool for quality control of DNA sequencing data

bioinformatics fastqc genomics sequencing wasm webassembly

Last synced: 05 Mar 2025

https://github.com/yanwu2014/swne

Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets

bioinformatics data-visualization dimensionality-reduction nonnegative-matrix-factorization single-cell-analysis single-cell-atac-seq single-cell-genomics single-cell-rna-seq statistical-methods

Last synced: 09 Apr 2025

https://github.com/baderlab/saber

Saber is a deep-learning based tool for information extraction in the biomedical domain. Pull requests are welcome! Note: this is a work in progress. Many things are broken, and the codebase is not stable.

bioinformatics biomedical-named-entity-recognition biomedical-text-mining deep-learning information-extraction machine-learning spacy