GitHub topics: bioconductor
Bioconductor/bioconductor_salt
Salt to configure Linux and Mac (x86_64, arm64) for the BBS
Language: SaltStack - Size: 256 KB - Last synced at: about 18 hours ago - Pushed at: about 19 hours ago - Stars: 1 - Forks: 3
adamurban04/DataPulse
DataPulse: Framework for Statistical and Exploratory Data Analysis
Language: R - Size: 28.2 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 0 - Forks: 0
tidyomics/tidySpatialWorkshop Fork of tidyomics/tidyomicsWorkshopBioc2023
Tidy spatial analyses workshop
Language: TeX - Size: 129 MB - Last synced at: 1 day ago - Pushed at: 1 day ago - Stars: 4 - Forks: 6
MoseleyBioinformaticsLab/categoryCompare2
Enables Gene Ontology (and other feature annotation) enrichment calculations and comparisons between feature sets.
Language: R - Size: 40.6 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 1 - Forks: 1
UCLouvain-CBIO/scp
Single cell proteomics data processing
Language: R - Size: 69.8 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 26 - Forks: 4
Dexwel/Dexwel
Daniel Adediran
Size: 109 KB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 0 - Forks: 0
bernatgel/regioneR
An R/Bioconfuctor package for association analysis of genomic regions based on permutation tests
Language: R - Size: 1.17 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 13 - Forks: 3
cmap/cmapR
Tools for manipulating annotated data matrices
Language: R - Size: 8.55 MB - Last synced at: 3 days ago - Pushed at: over 3 years ago - Stars: 92 - Forks: 34
Bioconductor/biocblog
A Quarto blog for Bioconductor community
Language: HTML - Size: 98.4 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 13 - Forks: 35
bernatgel/karyoploteR
karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
Language: R - Size: 3.07 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 312 - Forks: 41
SingleR-inc/SingleR
Clone of the Bioconductor repository for the SingleR package.
Language: R - Size: 1.4 MB - Last synced at: 2 days ago - Pushed at: 8 days ago - Stars: 191 - Forks: 19
GoekeLab/bambu
Reference-guided transcript discovery and quantification for long read RNA-Seq data
Language: R - Size: 549 MB - Last synced at: about 10 hours ago - Pushed at: 4 days ago - Stars: 210 - Forks: 24
sneumann/xcms
This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
Language: R - Size: 142 MB - Last synced at: 3 days ago - Pushed at: 4 days ago - Stars: 199 - Forks: 82
SingleR-inc/SingleRBook-base 📦
See https://github.com/LTLA/SingleRBook for the latest version of this content.
Language: TeX - Size: 91.8 KB - Last synced at: 4 days ago - Pushed at: almost 3 years ago - Stars: 11 - Forks: 8
lgatto/MSnbase
Base Classes and Functions for Mass Spectrometry and Proteomics
Language: R - Size: 108 MB - Last synced at: 2 days ago - Pushed at: about 2 months ago - Stars: 134 - Forks: 47
anushkasdeshmukh/rna-seq-airway-edger-analysis
Size: 260 KB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 0 - Forks: 0
waldronlab/curatedMetagenomicData
Curated Metagenomic Data of the Human Microbiome
Language: R - Size: 176 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 133 - Forks: 32
rformassspectrometry/RforMassSpectrometry.org
The R for Mass Spectrometry Initiative home page
Language: HTML - Size: 8.66 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 10 - Forks: 4
Bioconductor/EuroBioC2025
Website of the European Bioconductor Conference 2025
Language: CSS - Size: 10.8 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 2 - Forks: 4
theislab/anndata2ri
Convert between AnnData and SingleCellExperiment
Language: Python - Size: 242 KB - Last synced at: 8 days ago - Pushed at: 12 days ago - Stars: 134 - Forks: 19
sagrikachugh/simPIC
simPIC: simulating single cell ATAC-seq data
Language: R - Size: 5.86 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 0 - Forks: 0
rformassspectrometry/QFeatures
Quantitative features for mass spectrometry data
Language: R - Size: 27.5 MB - Last synced at: 6 days ago - Pushed at: 10 days ago - Stars: 27 - Forks: 8
microbiome/OMA
Orchestrating Microbiome Analysis
Language: TeX - Size: 1020 MB - Last synced at: 10 days ago - Pushed at: 10 days ago - Stars: 96 - Forks: 48
lmweber/OSTA
"Orchestrating Spatial Transcriptomics Analysis with Bioconductor" book
Language: TeX - Size: 65.7 MB - Last synced at: 9 days ago - Pushed at: 9 days ago - Stars: 78 - Forks: 29
mhahsler/rBLAST
Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package
Language: R - Size: 452 KB - Last synced at: 9 days ago - Pushed at: 5 months ago - Stars: 110 - Forks: 22
LieberInstitute/spatialLIBD
Code for the spatialLIBD R/Bioconductor package and shiny app
Language: R - Size: 263 MB - Last synced at: 6 days ago - Pushed at: 22 days ago - Stars: 93 - Forks: 20
neurogenomics/rworkflows
Continuous integration for R packages. 🔀 Automates testing ✅, documentation website building 📦, & containerised deployment 🐳.
Language: HTML - Size: 12.6 MB - Last synced at: 6 days ago - Pushed at: about 2 months ago - Stars: 80 - Forks: 7
BioinformaticsFMRP/TCGAbiolinks
TCGAbiolinks
Language: R - Size: 349 MB - Last synced at: 3 days ago - Pushed at: about 2 months ago - Stars: 318 - Forks: 117
LieberInstitute/recount3
Explore and download data from the recount3 project
Language: R - Size: 2.93 MB - Last synced at: 6 days ago - Pushed at: 16 days ago - Stars: 35 - Forks: 4
rformassspectrometry/Spectra
Low level infrastructure to handle MS spectra
Language: R - Size: 22.9 MB - Last synced at: 7 days ago - Pushed at: 11 days ago - Stars: 41 - Forks: 27
systemPipeR/systemPipeShiny
A Shiny framework for workflow management and data visualization
Language: R - Size: 26.2 MB - Last synced at: 7 days ago - Pushed at: 12 days ago - Stars: 34 - Forks: 6
grimbough/anaconda-download-stats
Process and host download statistics for Anaconda packages
Language: R - Size: 23 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 3 - Forks: 0
crisprVerse/crisprScore
On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs
Language: Python - Size: 80.8 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 20 - Forks: 4
RConsortium/r-advisory-database
Advisory database for R packages published on cran.r-project.org or bioconductor.org
Size: 33.2 KB - Last synced at: 7 days ago - Pushed at: 12 days ago - Stars: 13 - Forks: 4
Bioconductor/bioconductor_docker
Docker Containers for Bioconductor
Language: Dockerfile - Size: 382 KB - Last synced at: 6 days ago - Pushed at: 9 days ago - Stars: 79 - Forks: 32
tidyomics/omicslog
Log operations of R omic analyses
Language: R - Size: 35.2 KB - Last synced at: 14 days ago - Pushed at: 14 days ago - Stars: 0 - Forks: 0
seandavi/GEOquery
The bridge between the NCBI Gene Expression Omnibus and Bioconductor
Language: R - Size: 20.3 MB - Last synced at: 7 days ago - Pushed at: 7 months ago - Stars: 95 - Forks: 36
microbiome/mia
Microbiome analysis
Language: R - Size: 34.3 MB - Last synced at: 8 days ago - Pushed at: 16 days ago - Stars: 51 - Forks: 29
microbiome/miaViz
Microbiome Analysis Plotting and Visualization
Language: R - Size: 1.46 GB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 11 - Forks: 12
Bioconductor/bioconductor-training
Bioconductor teaching and education committee
Language: HTML - Size: 71.3 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 48 - Forks: 26
grimbough/bioc-actions
GitHub Actions for developing and maintaining Bioconductor packages
Language: R - Size: 120 KB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 12 - Forks: 3
Huber-group-EMBL/biomaRt
R package providing query functionality to BioMart instances like Ensembl
Language: R - Size: 2.31 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 43 - Forks: 16
biobakery/Maaslin2
MaAsLin2: Microbiome Multivariate Association with Linear Models
Language: R - Size: 1.19 MB - Last synced at: 14 days ago - Pushed at: 7 months ago - Stars: 138 - Forks: 35
datacamp/rdocumentation-2.0
📚 RDocumentation provides an easy way to search the documentation for every version of every R package on CRAN and Bioconductor.
Language: TypeScript - Size: 727 KB - Last synced at: 8 days ago - Pushed at: 3 months ago - Stars: 287 - Forks: 49
carpentries-incubator/bioc-rnaseq
Analysis and Interpretation of Bulk RNA-Seq Data using Bioconductor
Language: R - Size: 51.4 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 22 - Forks: 38
carpentries-incubator/bioc-intro
Bioconductor data science introduction
Language: R - Size: 741 MB - Last synced at: 12 days ago - Pushed at: 12 days ago - Stars: 27 - Forks: 33
Bioconductor/BiocStickers
Stickers for some Bioconductor packages - feel free to contribute and/or modify.
Language: R - Size: 385 MB - Last synced at: 8 days ago - Pushed at: 19 days ago - Stars: 125 - Forks: 89
Bioconductor/GenomicDataCommons
Provide R access to the NCI Genomic Data Commons portal.
Language: R - Size: 4.41 MB - Last synced at: 8 days ago - Pushed at: 19 days ago - Stars: 89 - Forks: 24
UCLouvain-CBIO/MDSvis
Interactive data exploration of Multi Dimensional Scaling (MDS) projections
Language: R - Size: 4.7 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 0 - Forks: 0
j-andrews7/ECLIPSE
An R package for classifying, comparing, and investigating sub-region structural changes of (super) enhancers (or other large domains).
Language: R - Size: 2.17 MB - Last synced at: 20 days ago - Pushed at: 21 days ago - Stars: 3 - Forks: 1
kdkorthauer/dmrseq
R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing
Language: R - Size: 22.9 MB - Last synced at: 22 days ago - Pushed at: 22 days ago - Stars: 58 - Forks: 14
stemangiola/tidybulk
Brings bulk and pseudobulk transcriptomics to the tidyverse
Language: R - Size: 99.4 MB - Last synced at: 17 days ago - Pushed at: about 2 months ago - Stars: 172 - Forks: 24
neurogenomics/EpiCompare
Comparison, benchmarking & QC of epigenetic datasets
Language: HTML - Size: 30.4 MB - Last synced at: 21 days ago - Pushed at: 3 months ago - Stars: 17 - Forks: 3
lcolladotor/bioc_team_ds
R/Bioconductor-powered Team Data Science by Leonardo Collado Torres
Language: HTML - Size: 3.26 MB - Last synced at: 18 days ago - Pushed at: 22 days ago - Stars: 3 - Forks: 4
federicomarini/GeneTonic
Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail
Language: R - Size: 121 MB - Last synced at: 8 days ago - Pushed at: 22 days ago - Stars: 78 - Forks: 10
seandavi/BiocPkgTools
Computable build reports, package metadata, and download stats from the Bioconductor project
Language: R - Size: 6.22 MB - Last synced at: 12 days ago - Pushed at: 23 days ago - Stars: 21 - Forks: 13
lcolladotor/DSgs_logs
Data Science guidance session logs
Language: R - Size: 6.5 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 0 - Forks: 0
pachterlab/voyager
From geospatial to spatial -omics
Language: R - Size: 4.32 GB - Last synced at: 17 days ago - Pushed at: 3 months ago - Stars: 92 - Forks: 11
waldronlab/HMP16SData
16S rRNA Sequencing Data from the Human Microbiome Project
Language: R - Size: 46.6 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 9 - Forks: 6
waldronlab/MultiAssayExperiment
Bioconductor package for management of multi-assay data
Language: R - Size: 5.56 MB - Last synced at: 26 days ago - Pushed at: 26 days ago - Stars: 72 - Forks: 34
JorgeAndOmics/RetroSeek
RetroSeek is a full object-oriented, parallelized, end-to-end computational pipeline designed to detect, categorize and annotate specified ERV integrations in genome assemblies. Built upon the Snakemake workflow management system, it is designed with a strong emphasis on parallelization, modularity, resilience, and reproducibility.
Language: Python - Size: 30.2 MB - Last synced at: 16 days ago - Pushed at: 16 days ago - Stars: 2 - Forks: 1
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/.
Language: R - Size: 26.9 MB - Last synced at: 13 days ago - Pushed at: 5 months ago - Stars: 4 - Forks: 0
Bioconductor/bioconductor.org
Source code for the Bioconductor website
Language: HTML - Size: 90.8 MB - Last synced at: 11 days ago - Pushed at: 26 days ago - Stars: 25 - Forks: 41
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: 461 KB - Last synced at: 6 days ago - Pushed at: 26 days ago - Stars: 72 - Forks: 20
zerostwo/shennong-object
🗂️Modern Data Structures for Multi-Omics Analysis
Language: R - Size: 74.2 KB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 0 - Forks: 0
rformassspectrometry/MsCoreUtils
Core Utils for Mass Spectrometry Data
Language: R - Size: 14.3 MB - Last synced at: 5 days ago - Pushed at: 2 months ago - Stars: 17 - Forks: 12
federicomarini/HCAData
Access data from the Human Cell Atlas project, directly via R/Bioconductor
Language: R - Size: 9.08 MB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 9 - Forks: 2
federicomarini/ideal
Interactive Differential Expression AnaLysis - DE made accessible and reproducible
Language: R - Size: 26.3 MB - Last synced at: 6 days ago - Pushed at: 29 days ago - Stars: 29 - Forks: 7
federicomarini/pcaExplorer
pcaExplorer - Interactive exploration of Principal Components of Samples and Genes in RNA-seq data
Language: R - Size: 60 MB - Last synced at: 8 days ago - Pushed at: 29 days ago - Stars: 56 - Forks: 17
federicomarini/flowcatchR
A framework for tracking and analyzing flowing blood cells in time lapse microscopy images
Language: R - Size: 24.9 MB - Last synced at: 29 days ago - Pushed at: 29 days ago - Stars: 4 - Forks: 0
thelovelab/fishpond
Differential expression and allelic analysis, nonparametric statistics
Language: R - Size: 7.89 MB - Last synced at: 15 days ago - Pushed at: 5 months ago - Stars: 29 - Forks: 10
benjjneb/dada2
Accurate sample inference from amplicon data with single nucleotide resolution
Language: R - Size: 468 MB - Last synced at: 26 days ago - Pushed at: about 2 months ago - Stars: 495 - Forks: 148
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.
Language: Jupyter Notebook - Size: 29.3 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0
carpentries-incubator/bioc-scrnaseq
Single-cell RNAseq materials derived from the 2023 ISMB OSCA workshop in the carpentries workbench format.
Language: R - Size: 883 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 3 - Forks: 2
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.
Language: TeX - Size: 478 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 9 - Forks: 12
mixOmicsTeam/mixOmics
Development repository for the Bioconductor package 'mixOmics '
Language: R - Size: 16.9 MB - Last synced at: 25 days ago - Pushed at: 25 days ago - Stars: 192 - Forks: 61
crisprVerse/crisprViz
Visualization of CRISPR guide RNAs (gRNAs)
Language: R - Size: 1.02 MB - Last synced at: 3 days ago - Pushed at: about 1 year ago - Stars: 9 - Forks: 0
saezlab/mistyR
Multiview Intercellular SpaTial modeling framework
Language: R - Size: 126 MB - Last synced at: about 1 month ago - Pushed at: about 1 year ago - Stars: 54 - Forks: 11
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: 15 days ago - Pushed at: over 1 year ago - Stars: 26 - Forks: 17
LieberInstitute/DeconvoBuddies
Helper Functions for LIBD Deconvolution
Language: R - Size: 63.3 MB - Last synced at: 10 days ago - Pushed at: 2 months ago - Stars: 5 - Forks: 1
theislab/zellkonverter
Conversion between scRNA-seq objects
Language: R - Size: 2.02 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 171 - Forks: 29
Oshlack/splatter
Simple simulation of single-cell RNA sequencing data
Language: R - Size: 57.2 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 226 - Forks: 57
schifferl/MultimodalExperiment
Integrative Bulk and Single-Cell Experiment Container
Language: R - Size: 2.92 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0
schifferl/tuberculosis
Tuberculosis Gene Expression Data for Machine Learning
Language: R - Size: 87.9 KB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 3 - Forks: 0
metamaden/metamaden.github.io
Professional resume, portfolio, bio, and presentations for Sean K. Maden, Ph.D.
Language: HTML - Size: 39.4 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 0 - Forks: 0
shgopher/RFamily
R 语言基础，数据分析， 可视化，生物以及临床医学研究
Language: Shell - Size: 15.6 KB - Last synced at: 7 days ago - Pushed at: 9 months ago - Stars: 2 - Forks: 0
acinostroza/TargetSearchData
Example GC-MS data for TargetSearch Package
Language: TeX - Size: 29.1 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 1
acinostroza/TargetSearch
R package for the analysis of GC-MS metabolite profiling data. This git repository mirrors the TargetSearch git repository on bioconductor.
Language: R - Size: 1.04 MB - Last synced at: 12 days ago - Pushed at: about 1 month ago - Stars: 4 - Forks: 0
ComputationalProteomics/NormalyzerDE
Tools for normalization, evaluation of outliers, technical biases and batch effects and differential expression analysis.
Language: R - Size: 6 MB - Last synced at: 5 days ago - Pushed at: 8 months ago - Stars: 23 - Forks: 6
CarlosUziel/goi-strat
GoiStrat - A novel supervised approach to gene of interest based sample stratification and analysis to assess biological differences
Language: Python - Size: 20.8 MB - Last synced at: about 2 months ago - Pushed at: about 2 months ago - Stars: 2 - Forks: 1
Bioconductor/Contributions
Contribute Packages to Bioconductor
Size: 58.6 KB - Last synced at: 22 days ago - Pushed at: about 2 months ago - Stars: 136 - Forks: 34
lgatto/pRoloc
A unifying bioinformatics framework for organelle proteomics
Language: R - Size: 252 MB - Last synced at: 6 days ago - Pushed at: about 2 months ago - Stars: 16 - Forks: 14
BBCG/epialleleR
Fast, epiallele-aware methylation caller and reporter — an R/Bioconductor package
Language: R - Size: 82.7 MB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 6 - Forks: 1
lcolladotor/biocthis
Automate package and project setup for Bioconductor packages
Language: R - Size: 1.16 MB - Last synced at: 17 days ago - Pushed at: 2 months ago - Stars: 53 - Forks: 17
Bioconductor/bioc_coc_multilingual
Multilingual version of the Bioconductor Code of Conduct
Language: CSS - Size: 1.46 MB - Last synced at: about 1 month ago - Pushed at: about 2 months ago - Stars: 2 - Forks: 17
rformassspectrometry/MsDataHub
Mass Spectrometry Data on ExperimentHub
Language: R - Size: 297 KB - Last synced at: 16 days ago - Pushed at: about 2 months ago - Stars: 1 - Forks: 1
BioGenies/tidysq
tidy processing of biological sequences in R
Language: C++ - Size: 10.9 MB - Last synced at: 3 days ago - Pushed at: 5 months ago - Stars: 42 - Forks: 4
mikelove/bioc-refcard
Bioconductor cheat sheet
Language: HTML - Size: 376 KB - Last synced at: about 1 month ago - Pushed at: 9 months ago - Stars: 188 - Forks: 66
BiodataAnalysisGroup/tripr
T-cell Receptor/Immunoglobulin Profiler {tripr}
Language: R - Size: 10.4 MB - Last synced at: 15 days ago - Pushed at: about 2 months ago - Stars: 2 - Forks: 4
nuno-agostinho/psichomics
Interactive R package to quantify, analyse and visualise alternative splicing
Language: R - Size: 59.1 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 37 - Forks: 11
