GitHub topics: bioconductor
theislab/zellkonverter
Conversion between scRNA-seq objects
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Oshlack/splatter
Simple simulation of single-cell RNA sequencing data
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schifferl/MultimodalExperiment
Integrative Bulk and Single-Cell Experiment Container
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schifferl/tuberculosis
Tuberculosis Gene Expression Data for Machine Learning
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metamaden/metamaden.github.io
Professional resume, portfolio, bio, and presentations for Sean K. Maden, Ph.D.
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seandavi/GEOquery
The bridge between the NCBI Gene Expression Omnibus and Bioconductor
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mixOmicsTeam/mixOmics
Development repository for the Bioconductor package 'mixOmics '
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waldronlab/HMP16SData
16S rRNA Sequencing Data from the Human Microbiome Project
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waldronlab/curatedMetagenomicData
Curated Metagenomic Data of the Human Microbiome
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waldronlab/MultiAssayExperiment
Bioconductor package for management of multi-assay data
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Bioconductor/GenomicDataCommons
Provide R access to the NCI Genomic Data Commons portal.
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acinostroza/TargetSearchData
Example GC-MS data for TargetSearch Package
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acinostroza/TargetSearch
R package for the analysis of GC-MS metabolite profiling data. This git repository mirrors the TargetSearch git repository on bioconductor.
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microbiome/OMA
Orchestrating Microbiome Analysis
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Bioconductor/bioconductor_docker
Docker Containers for Bioconductor
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lpantano/DEGreport
Create a cromphensive report of DEG list coming from any analysis of RNAseq data
Language: R - Size: 51.7 MB - Last synced at: 4 days ago - Pushed at: about 1 year ago - Stars: 25 - Forks: 16
CarlosUziel/goi-strat
GoiStrat - A novel supervised approach to gene of interest based sample stratification and analysis to assess biological differences
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lgatto/MSnbase
Base Classes and Functions for Mass Spectrometry and Proteomics
Language: R - Size: 108 MB - Last synced at: 6 days ago - Pushed at: 10 days ago - Stars: 131 - Forks: 46
systemPipeR/systemPipeShiny
A Shiny framework for workflow management and data visualization
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GoekeLab/bambu
Reference-guided transcript discovery and quantification for long read RNA-Seq data
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federicomarini/GeneTonic
Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail
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LieberInstitute/DeconvoBuddies
Helper Functions for LIBD Deconvolution
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Bioconductor/Contributions
Contribute Packages to Bioconductor
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grimbough/bioc-actions
GitHub Actions for developing and maintaining Bioconductor packages
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lcolladotor/biocthis
Automate package and project setup for Bioconductor packages
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Huber-group-EMBL/biomaRt
R package providing query functionality to BioMart instances like Ensembl
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BioinformaticsFMRP/TCGAbiolinks
TCGAbiolinks
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theislab/anndata2ri
Convert between AnnData and SingleCellExperiment
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rformassspectrometry/Spectra
Low level infrastructure to handle MS spectra
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seandavi/BiocPkgTools
Computable build reports, package metadata, and download stats from the Bioconductor project
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rformassspectrometry/MsDataHub
Mass Spectrometry Data on ExperimentHub
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pachterlab/voyager
From geospatial to spatial -omics
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BioGenies/tidysq
tidy processing of biological sequences in R
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Bioconductor/bioconductor.org
Source code for the Bioconductor website
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stemangiola/tidybulk
Brings bulk and pseudobulk transcriptomics to the tidyverse
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LieberInstitute/visiumStitched
R package containing functions useful for stitching Visium capture areas. Related to the example human brain data described at http://research.libd.org/visiumStitched_brain/.
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benjjneb/dada2
Accurate sample inference from amplicon data with single nucleotide resolution
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BiodataAnalysisGroup/tripr
T-cell Receptor/Immunoglobulin Profiler {tripr}
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ebi-gene-expression-group/bioconductor-ExpressionAtlas
Download datasets from EMBL-EBI Expression Atlas
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LieberInstitute/spatialLIBD
Code for the spatialLIBD R/Bioconductor package and shiny app
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wejlab/LegATo
An R-based Longitudinal mEtaGenomic Analysis Toolkit for microbiome data
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Bioconductor/bioconductor_salt
Salt to configure Linux and Mac (x86_64, arm64) for the BBS
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mhahsler/rBLAST
Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package
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carpentries-incubator/bioc-intro
Bioconductor data science introduction
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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).
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Bioconductor/bioc_coc_multilingual
Multilingual version of the Bioconductor Code of Conduct
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lcolladotor/DSgs_logs
Data Science guidance session logs
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adamurban04/OncoEx
OncoEx: Framework for Statistical and Exploratory Data Analysis
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iSEE/iSEE.github.io
Quarto website
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microbiome/mia
Microbiome analysis
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rformassspectrometry/QFeatures
Quantitative features for mass spectrometry data
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carpentries-incubator/bioc-project
Introduction to the Bioconductor project
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biobakery/Maaslin2
MaAsLin2: Microbiome Multivariate Association with Linear Models
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Bioconductor/EuroBioC2025
Website of the European Bioconductor Conference 2025
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lgatto/RforProteomics
Using R and Bioconductor packages for the analysis and comprehension of proteomics data.
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lgatto/pRoloc
A unifying bioinformatics framework for organelle proteomics
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datacamp/rdocumentation-2.0
📚 RDocumentation provides an easy way to search the documentation for every version of every R package on CRAN and Bioconductor.
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pmb59/bioconductor-ci-validator
Bioconductor package validator via Continuous Integration
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HenrikBengtsson/affxparser
🔬 R package: This is the Bioconductor devel version of the affxparser package.
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Bioconductor/bioconductor-training
Bioconductor teaching and education committee
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lmweber/OSTA
"Orchestrating Spatial Transcriptomics Analysis with Bioconductor" book
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LieberInstitute/recount3
Explore and download data from the recount3 project
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cmap/cmapR
Tools for manipulating annotated data matrices
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Huber-group-EMBL/Rhdf5lib
Distribution of the HDF5 library in an R package
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Bioconductor/BiocStickers
Stickers for some Bioconductor packages - feel free to contribute and/or modify.
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rformassspectrometry/MsCoreUtils
Core Utils for Mass Spectrometry Data
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LieberInstitute/spatialDLPFC
spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples
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colossal-compsci/tfboot
R package for bootstrapping motifbreakR results
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lcolladotor/derfinder
Annotation-agnostic differential expression analysis of RNA-seq data via expressed regions-level or single base-level approaches
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grimbough/anaconda-download-stats
Process and host download statistics for Anaconda packages
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MicrobialGenomics-IrsicaixaOrg/dar
dar: runs multiple differential abundance analysis methods and through a consensus strategy returns a set of differentially abundant features.
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microbiome/miaViz
Microbiome Analysis Plotting and Visualization
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FelixErnst/Structstrings
:package: Structstrings: implementation of Biostrings to work with dot bracket annotations
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saezlab/mistyR
Multiview Intercellular SpaTial modeling framework
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lcolladotor/bioc_team_ds
R/Bioconductor-powered Team Data Science by Leonardo Collado Torres
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sneumann/xcms
This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
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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.
Language: R - Size: 459 KB - Last synced at: 14 days ago - Pushed at: about 1 month ago - Stars: 71 - Forks: 20
bernatgel/karyoploteR
karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
Language: R - Size: 3.06 MB - Last synced at: about 1 month ago - Pushed at: over 1 year ago - Stars: 307 - Forks: 41
LieberInstitute/DLPFC_snRNAseq
snRNA_seq portion of the spatialDLPFC project
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carpentries-incubator/bioc-scrnaseq
Single-cell RNAseq materials derived from the 2023 ISMB OSCA workshop in the carpentries workbench format.
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UCLouvain-CBIO/MDSvis
Interactive exploring Multi Dimensional Scaling projections
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tidyomics/plyranges
A grammar of genomic data transformation
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seandavi/refinebioc
The bridge between refine.bio and Bioconductor
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mhahsler/rRDP
Seamlessly interfaces RDP classifier.
Language: R - Size: 2.86 MB - Last synced at: 21 days ago - Pushed at: 12 months ago - Stars: 3 - Forks: 1
UCLouvain-CBIO/LSTAT2340
Traitement statistique de données omiques
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federicomarini/HCAData
Access data from the Human Cell Atlas project, directly via R/Bioconductor
Language: R - Size: 9.06 MB - Last synced at: 5 days ago - Pushed at: about 1 month ago - Stars: 9 - Forks: 2
federicomarini/pcaExplorer
pcaExplorer - Interactive exploration of Principal Components of Samples and Genes in RNA-seq data
Language: R - Size: 59.9 MB - Last synced at: 8 days ago - Pushed at: about 1 month ago - Stars: 56 - Forks: 17
federicomarini/flowcatchR
A framework for tracking and analyzing flowing blood cells in time lapse microscopy images
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federicomarini/ideal
Interactive Differential Expression AnaLysis - DE made accessible and reproducible
Language: R - Size: 26.2 MB - Last synced at: 15 days ago - Pushed at: about 1 month ago - Stars: 29 - Forks: 7
crisprVerse/crisprViz
Visualization of CRISPR guide RNAs (gRNAs)
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crisprVerse/crisprDesign
Comprehensive design of CRISPR gRNAs for nucleases and base editors
Language: R - Size: 5.93 MB - Last synced at: 14 days ago - Pushed at: about 2 months ago - Stars: 22 - Forks: 6
carpentries-incubator/bioc-rnaseq
Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor
Language: R - Size: 53.1 MB - Last synced at: 18 days ago - Pushed at: 3 months ago - Stars: 22 - Forks: 36
Akmagan387/bioconductor-learning-container
🧬 Containerized development environment for Harvard's Professional Certificate in Data Analysis for Genomics (PH525.x series). Streamlined setup for Bioconductor, R, and genomic data analysis with RStudio and DevContainer support.
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NikitaArya17/next_generation_sequencing_projects
A collection of independent research projects involving various methods involving next generation sequencing (NGS) data analysis, including scRNA-seq, RNA-seq and scATAC-seq data.
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rformassspectrometry/RforMassSpectrometry.org
The R for Mass Spectrometry Initiative home page
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LTLA/scRNAseq
Clone of the Bioconductor repository for the scRNAseq package.
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ilia-kats/MuData
MuData-compatible storage for bioconductor's MultiAssayExperiment
Language: R - Size: 8.58 MB - Last synced at: 9 days ago - Pushed at: about 2 months ago - Stars: 5 - Forks: 4
ferygood/TEKRABber
An R Bioinformatic package for DE and correlation analysis comparing between species.
Language: R - Size: 10.3 MB - Last synced at: 27 days ago - Pushed at: about 2 months ago - Stars: 3 - Forks: 0
kozo2/AHPathbankDbs
Supplies AnnotationHub with Pathbank-based annotation databases for all species.
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Bioconductor/BiocWorkingGroups
Bioconductor working group guidelines. Also, a list of active, suggested, and inactive working groups for bioconductor for the community to volunteer to be apart of. The community is also welcome to suggest new working groups.
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