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Awesome

An open API service indexing awesome lists of open source software.

Projects in Awesome Lists tagged with bioconductor

A curated list of projects in awesome lists tagged with bioconductor .

https://github.com/benjjneb/dada2

Accurate sample inference from amplicon data with single nucleotide resolution

amplicon bioconductor bioinformatics metabarcoding metagenomics microbiome taxonomy

Last synced: 18 Feb 2026

https://github.com/bernatgel/karyoploter

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

bioconductor bioinformatics data-visualization genome genomics-visualization plotting-in-r rstats

Last synced: 19 Jul 2025

https://github.com/bernatgel/karyoploteR

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

bioconductor bioinformatics data-visualization genome genomics-visualization plotting-in-r rstats

Last synced: 07 May 2025

https://github.com/datacamp/rdocumentation-2.0

📚 RDocumentation provides an easy way to search the documentation for every version of every R package on CRAN and Bioconductor.

bioconductor cran documentation packages rstats

Last synced: 05 Oct 2025

https://github.com/GoekeLab/bambu

Reference-guided transcript discovery and quantification for long read RNA-Seq data

bambu bioconductor long-reads nanopore nanopore-sequencing r rna-seq rna-seq-analysis transcript-quantification transcript-reconstruction transcriptomics

Last synced: 06 May 2025

https://github.com/sneumann/xcms

This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis

bioconductor feature-detection mass-spectrometry metabolomics peak-detection r

Last synced: 14 May 2025

https://github.com/SingleR-inc/SingleR

Clone of the Bioconductor repository for the SingleR package.

bioconductor singler

Last synced: 29 Jul 2025

https://github.com/singler-inc/singler

Clone of the Bioconductor repository for the SingleR package.

bioconductor singler

Last synced: 06 Oct 2025

https://github.com/goekelab/bambu

Reference-guided transcript discovery and quantification for long read RNA-Seq data

bambu bioconductor long-reads nanopore nanopore-sequencing r rna-seq rna-seq-analysis transcript-quantification transcript-reconstruction transcriptomics

Last synced: 15 May 2025

https://github.com/tidyomics/plyranges

A grammar of genomic data transformation

bioconductor data-analysis dplyr genomic-ranges genomics tidy-data

Last synced: 06 Feb 2026

https://github.com/thelovelab/tximport

Transcript quantification import for modular pipelines

bioconductor deseq2 rnaseq

Last synced: 20 Oct 2025

https://github.com/bioconductor/contributions

Contribute Packages to Bioconductor

bioconductor

Last synced: 14 Jun 2025

https://github.com/Bioconductor/Contributions

Contribute Packages to Bioconductor

bioconductor

Last synced: 09 May 2025

https://github.com/theislab/anndata2ri

Convert between AnnData and SingleCellExperiment

bioconductor jupyter rpy2 scanpy single-cell

Last synced: 16 May 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: 15 May 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: 30 Apr 2025

https://github.com/bioconductor/biocstickers

Stickers for some Bioconductor packages - feel free to contribute and/or modify.

bioconductor stickers

Last synced: 12 Apr 2025

https://github.com/Bioconductor/BiocStickers

Stickers for some Bioconductor packages - feel free to contribute and/or modify.

bioconductor stickers

Last synced: 09 May 2025

https://github.com/mhahsler/rblast

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

bioconductor bioinformatics blast-search

Last synced: 16 May 2025

https://github.com/lmweber/osta

"Orchestrating Spatial Transcriptomics Analysis with Bioconductor" (OSTA) online book

analysis-workflows bioconductor spatial-transcriptomics spatially-resolved-transcriptomics

Last synced: 26 Jan 2026

https://github.com/lieberinstitute/spatiallibd

Code for the spatialLIBD R/Bioconductor package and shiny app

10xgenomics bioconductor golem rstats shiny spatial-transcriptomics spatialexperiment spatiallibd visium

Last synced: 06 Oct 2025

https://github.com/microbiome/oma

Orchestrating Microbiome Analysis

bioconductor microbiome microbiome-analysis-book r

Last synced: 16 May 2025

https://github.com/cmap/cmapr

Tools for manipulating annotated data matrices

bioconductor bioinformatics cmap

Last synced: 20 Feb 2026

https://github.com/lgatto/rforproteomics

Using R and Bioconductor packages for the analysis and comprehension of proteomics data.

bioconductor bioconductor-packages mass-spectrometry proteomics proteomics-data r tutorial

Last synced: 17 Mar 2025

https://github.com/seandavi/geoquery

The bridge between the NCBI Gene Expression Omnibus and Bioconductor

bioconductor bioinformatics data-science genomics ncbi-geo r rstats

Last synced: 04 Apr 2025

https://github.com/teunbrand/ggnomics

A small project to add ggplot2 extensions

bioconductor genomics ggplot-extension visualization

Last synced: 18 Jul 2025

https://github.com/neurogenomics/rworkflows

Continuous integration for R packages. 🔀 Automates testing ✅, documentation website building 📦, & containerised deployment 🐳.

bioconductor containers continuous-integration cran-r docker dockerhub github-actions r reproducibility workflows

Last synced: 05 Apr 2025

https://github.com/bioconductor/bioconductor_docker

Docker Containers for Bioconductor - NEW!

bioconductor bioconductor-containers docker-image

Last synced: 08 May 2025

https://github.com/drisso/singlecellexperiment

Clone of the Bioconductor repository for the SingleCellExperiment package, see https://bioconductor.org/packages/devel/bioc/html/SingleCellExperiment.html for the official development version.

bioconductor bioconductor-package human-cell-atlas single-cell-rna-seq

Last synced: 06 Apr 2025

https://github.com/kdkorthauer/dmrseq

R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing

bioconductor bisulfite-sequencing dmr epigenetics inference methylation

Last synced: 21 Feb 2026

https://github.com/federicomarini/pcaexplorer

pcaExplorer - Interactive exploration of Principal Components of Samples and Genes in RNA-seq data

bioconductor principal-components r reproducible-research rna-seq-analysis rna-seq-data shiny transcriptome user-friendly

Last synced: 13 Apr 2025

https://github.com/lcolladotor/biocthis

Automate package and project setup for Bioconductor packages

actions bioconductor biocthis github rstats styler usethis

Last synced: 11 Oct 2025

https://lcolladotor.github.io/biocthis/

Automate package and project setup for Bioconductor packages

actions bioconductor biocthis github rstats styler usethis

Last synced: 24 Apr 2025

https://github.com/microbiome/mia

Microbiome analysis

analysis bioconductor microbiome

Last synced: 16 May 2025

https://github.com/bioinformaticsfmrp/tcgaworkflow

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages

bioconductor tcga tcgabiolinks

Last synced: 23 Jan 2026

https://github.com/bioconductor/bioconductor-training

Bioconductor teaching and education committee

bioconductor committee education teaching training

Last synced: 27 Jan 2026

https://github.com/neurogenomics/orthogene

🧬 o r t h o g e n e 🧬✨✨✨✨✨✨✨ Interspecies gene mapping✨✨✨✨✨ 🦠 🔁 🌱 🔁 🌳 🔁 🍎 🔁 🍊 🔁 🪱 🔁 🪰 🔁 🐟 🔁 🦎 🔁 🐓 🔁 🦇 🔁 🐄 🔁 🐖 🔁 🐐 🔁 🐎 🔁 🐈 🔁 🐕 🔁 🐁 🔁 🐒 🔁 🦧 🔁 🦍 🔁 🏃‍♀️

animal-models bioconductor bioconductor-package bioinformatics biomedicine comparative-genomics evolutionary-biology genes genomics ontologies r r-package translational-research

Last synced: 14 Oct 2025

https://github.com/huber-group-embl/biomart

R package providing query functionality to BioMart instances like Ensembl

bioconductor biomart ensembl r

Last synced: 17 Aug 2025

https://github.com/lcolladotor/derfinder

Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches

annotation-agnostic bioconductor derfinder r rnaseq rstats

Last synced: 13 Apr 2025

https://github.com/plger/pipecomp

A R framework for pipeline benchmarking, with application to single-cell RNAseq

benchmark bioconductor clustering pipeline-benchmarking pipelines single-cell-rna-seq

Last synced: 07 May 2025

https://github.com/bioinformatics-core-shared-training/ngs-in-bioc

A course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor

bioconductor ngs rna-seq training

Last synced: 02 Apr 2025

https://github.com/grimbough/biomart

R package providing query functionality to BioMart instances like Ensembl

bioconductor biomart ensembl r

Last synced: 13 Mar 2025

https://github.com/rformassspectrometry/spectra

Low level infrastructure to handle MS spectra

bioconductor mass-spectrometry metabolomics proteomics rstats

Last synced: 04 Apr 2025

https://github.com/nanxstats/rcpi

💊 Molecular informatics toolkit with integration of bioinformatics and cheminformatics tools for drug discovery

bioconductor bioinformatics cheminformatics drug-discovery feature-extraction fingerprint molecular-descriptors protein-sequences

Last synced: 22 Aug 2025

https://rformassspectrometry.github.io/Spectra/

Low level infrastructure to handle MS spectra

bioconductor mass-spectrometry metabolomics proteomics rstats

Last synced: 13 Apr 2025

https://github.com/sbg/sevenbridges-r

Seven Bridges API Client, CWL Schema, Meta Schema, and SDK Helper in R

api-client bioconductor bioinformatics cloud common-workflow-language sevenbridges

Last synced: 19 Feb 2026

https://github.com/biobakery/melonnpan

Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles

biobakery bioconductor machine-learning metabolite-compounds metabolite-prediction metabolomics metagenomics microbial-communities microbiome multi-omics public tools

Last synced: 30 Oct 2025

https://github.com/bioinformaticsfmrp/tcgabiolinksgui

TCGAbiolinksGUI code development for R/Bioconductor submission http://tcgabiolinks.fmrp.usp.br:3838/

bioconductor gdc gui integrative r tcga-data tcgabiolinks

Last synced: 01 Sep 2025

https://github.com/systemPipeR/systemPipeShiny

A Shiny framework for workflow management and data visualization

bioconductor bioconductor-package data-visualization r shiny systempiper

Last synced: 30 Jul 2025

https://github.com/jorainer/ensembldb

This is the ensembldb development repository.

annotation bioconductor bioconductor-packages ensembl

Last synced: 10 Apr 2025

https://github.com/ahmohamed/lipidr

Data Mining and Analysis of Lipidomics datasets in R

bioconductor lipidomics r

Last synced: 21 Feb 2026

https://github.com/federicomarini/ideal

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

bioconductor differential-expression r reproducible-research rna-seq rna-seq-analysis shiny user-friendly

Last synced: 06 Apr 2025

https://github.com/bodenmillergroup/imcdataanalysis

R based workflow for multiplexed imaging data

bioconductor image-analysis single-cell spatial-analysis

Last synced: 07 Sep 2025

https://github.com/rformassspectrometry/qfeatures

Quantitative features for mass spectrometry data

bioconductor mass-spectrometry metabolomics proteomics rstats

Last synced: 06 Apr 2025

https://github.com/nullranges/nullranges

Modular package for generation of sets of ranges representing the null hypothesis. These can take the form of bootstrapped ranges (bootRanges), or set of control ranges that are matched across one or more covariates (matchRanges).

bioconductor bootstrap genomics matching statistics

Last synced: 10 Apr 2025

https://github.com/bioconductor/bioconductor_full

DEPRECATED - Docker Images which include a complete installation of all software needed to build all Bioconductor packages

bioconductor containers docker

Last synced: 28 Apr 2025

https://github.com/bioconductor/bioconductor.org

Source code for the Bioconductor website

bioconductor website

Last synced: 26 Feb 2025

https://rformassspectrometry.github.io/QFeatures/

Quantitative features for mass spectrometry data

bioconductor mass-spectrometry metabolomics proteomics rstats

Last synced: 13 Apr 2025

https://github.com/aoles/rbioformats

:books: R interface to the Bio-Formats library

bio-formats bioconductor image-processing r

Last synced: 16 Mar 2026

https://github.com/ltla/scrnaseq

Clone of the Bioconductor repository for the scRNAseq package.

bioconductor

Last synced: 10 Apr 2025

https://github.com/mikelove/alpine

Modeling and correcting fragment sequence bias for RNA-seq

bioconductor rnaseq

Last synced: 17 Sep 2025

https://github.com/lpantano/degreport

Create a cromphensive report of DEG list coming from any analysis of RNAseq data

bioconductor differential-expression qc r report rna-seq smallrna

Last synced: 17 Mar 2025

https://github.com/uclouvain-cbio/depmap

Cancer Dependency Map package

bioconductor bioconductor-package depmap

Last synced: 28 Oct 2025

https://github.com/lieberinstitute/spatialdlpfc

spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples

bioconductor dlpfc rstats spatial-transcriptomics spatialdlpfc transcriptomics visium visium-spg

Last synced: 31 Jan 2026

https://github.com/dieterich-lab/circtools

circtools: a modular, python-based framework for circRNA-related tools that unifies several functionalities in a single, command line driven software.

bioconductor bioinformatics circular-rna computational-rna-biology dcc fuchs primer-design rbp toolbox

Last synced: 25 Jan 2026

https://github.com/seandavi/biocpkgtools

Computable build reports, package metadata, and download stats from the Bioconductor project

bioconductor metadata rstats

Last synced: 07 Apr 2025

https://github.com/Appsilon/shiny.gosling

R Shiny wrapper for Gosling.js - Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization

bioconductor genomics-visualization r shiny

Last synced: 20 Jul 2025

https://github.com/darwinawardwinner/cd4-csaw

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

bioconductor bioinformatics-pipeline chip-seq r reproducible-research rna-seq

Last synced: 23 Apr 2025

https://github.com/lgatto/proloc

A unifying bioinformatics framework for organelle proteomics

bioconductor proteomics proteomics-data r spatial-proteomics visualisation

Last synced: 06 Apr 2025

https://github.com/bioconductor/bioc_git_transition

This python package is for transitioning bioconductor from SVN to git

bioconductor git svn2git

Last synced: 28 Apr 2025

https://github.com/Marlin-Na/TnT

Interactive visulizations for track-based genomic data in R

bioconductor genome-browser htmlwidgets r shiny

Last synced: 08 May 2025

https://github.com/marlin-na/tnt

Interactive visulizations for track-based genomic data in R

bioconductor genome-browser htmlwidgets r shiny

Last synced: 21 Aug 2025

https://github.com/matthewcarlucci/discorhythm

An R Package for Discovering Rhythmicity in Biological Data with an Interactive Web Interface

bioconductor data-visualization oscillations package r rhythm-detection webapp

Last synced: 23 Jun 2025

https://github.com/cbg-ethz/dce

Finding the causality in biological pathways

bioconductor causality r

Last synced: 28 Apr 2025