bioconductor

There are 15 repositories under bioconductor topic.

benjjneb / dada2
Accurate sample inference from amplicon data with single nucleotide resolution
amplicon bioconductor bioinformatics metabarcoding metagenomics microbiome taxonomy
Language:R 464
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
Language:R 296
BioinformaticsFMRP / TCGAbiolinks
TCGAbiolinks
integrative-analysis bioc r tcgabiolinks bioconductor gdc tcga tcga-data
Language:R 289
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
Language:TypeScript 282
splatter
Oshlack / splatter
Simple simulation of single-cell RNA sequencing data
bioconductor simulation scrna-seq bioinformatics
Language:R 213
mikelove / bioc-refcard
Bioconductor cheat sheet
bioconductor bioinformatics r rnaseq compbio guide howto cheatsheet microarray
Language:HTML 186
sneumann / xcms
This is the git repository matching the Bioconductor package xcms: LC/MS and GC/MS Data Analysis
bioconductor metabolomics mass-spectrometry peak-detection feature-detection r
Language:R 182
bambu
GoekeLab / bambu
Reference-guided transcript discovery and quantification for long read RNA-Seq data
bambu transcript-reconstruction transcript-quantification long-reads nanopore-sequencing transcriptomics rna-seq-analysis bioconductor r nanopore rna-seq
Language:R 180
SingleR-inc / SingleR
Clone of the Bioconductor repository for the SingleR package.
bioconductor singler
Language:R 172
tidybulk
stemangiola / tidybulk
Brings bulk and pseudobulk transcriptomics to the tidyverse
tidyverse tidy tidy-data bioconductor edger deseq2 transcriptomics pipe tibble gene-symbols bulk-transcriptional-analyses mds-dimensions ensembl-ids transcripts tsne pca redundancy entrez gsea differential-expression
Language:R 164
mixOmics
mixOmicsTeam / mixOmics
Development repository for the Bioconductor package 'mixOmics '
r r-package rstats rstats-package r-project r-pkg bioconductor genomics genomics-visualization genomics-data omics multivariate-analysis multivariate-statistics
Language:R 155
theislab / zellkonverter
Conversion between scRNA-seq objects
bioconductor conversion r scrna-seq
Language:R 146
tidyomics / plyranges
A grammar of genomic data transformation
bioconductor data-analysis dplyr genomic-ranges genomics tidy-data
Language:R 137
Bioconductor / Contributions
Contribute Packages to Bioconductor
bioconductor
134
thelovelab / tximport
Transcript quantification import for modular pipelines
rnaseq bioconductor deseq2
Language:R 134
waldronlab / curatedMetagenomicData
Curated Metagenomic Data of the Human Microbiome
bioconductor bioconductor-package experimenthub
Language:R 125
lgatto / MSnbase
Base Classes and Functions for Mass Spectrometry and Proteomics
bioconductor mass-spectrometry r proteomics bioinformatics proteomics-data visualisation
Language:R 124
theislab / anndata2ri
Convert between AnnData and SingleCellExperiment
bioconductor jupyter rpy2 scanpy single-cell
Language:Python 124
Bioconductor / BiocStickers
Stickers for some Bioconductor packages - feel free to contribute and/or modify.
bioconductor stickers
Language:R 122
biobakery / Maaslin2
MaAsLin2: Microbiome Multivariate Association with Linear Models
biobakery public tools bioconductor microbiome metagenomics differential-abundance-analysis false-discovery-rate repeated-measures multiple-covariates
Language:R 112
mhahsler / rBLAST
Interface for the Basic Local Alignment Search Tool (BLAST) - R-Package
bioconductor bioinformatics blast-search
Language:R 103
seandavi / GEOquery
The bridge between the NCBI Gene Expression Omnibus and Bioconductor
bioinformatics ncbi-geo bioconductor r rstats data-science genomics
Language:R 87
Bioconductor / GenomicDataCommons
Provide R access to the NCI Genomic Data Commons portal.
tcga nci bioconductor vignette cancer genomics bioinformatics r api-client data-science core-services
Language:R 84
cmap / cmapR
Tools for manipulating annotated data matrices
bioconductor cmap bioinformatics
Language:R 84
microbiome / OMA
Orchestrating Microbiome Analysis
microbiome microbiome-analysis-book r bioconductor
Language:TeX 84
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
Language:TeX 83
LieberInstitute / spatialLIBD
Code for the spatialLIBD R/Bioconductor package and shiny app
rstats shiny spatial-transcriptomics 10xgenomics bioconductor golem visium spatialexperiment spatiallibd
Language:R 80
teunbrand / ggnomics
A small project to add ggplot2 extensions
ggplot-extension genomics bioconductor visualization
Language:R 80
federicomarini / GeneTonic
Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail
rna-seq-data rna-seq-analysis transcriptomics r shiny transcriptome reproducible-research gui user-friendly bioconductor bioconductor-package functional-enrichment-analysis pathway-analysis gene-expression data-visualization data-exploration
Language:R 75
Bioconductor / bioconductor_docker
Docker Containers for Bioconductor - NEW!
bioconductor bioconductor-containers docker-image
Language:Shell 73
rworkflows
neurogenomics / rworkflows
Continuous integration for R packages. 🔀 Automates testing ✅, documentation website building 📦, & containerised deployment 🐳.
docker dockerhub github-actions continuous-integration containers r bioconductor reproducibility workflows cran-r
Language:HTML 73
pachterlab / voyager
From geospatial to spatial -omics
bioconductor eda esda exploratory-data-analysis omics r r-package rstats spatial spatial-statistics spatial-transcriptomics transcriptomics
Language:R 70
waldronlab / MultiAssayExperiment
Bioconductor package for management of multi-assay data
bioconductor r tcga genomics nci-itcr bioconductor-package
Language:R 69
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.
human-cell-atlas bioconductor single-cell-rna-seq bioconductor-package
Language:R 65
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
Language:R 54
kdkorthauer / dmrseq
R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing
bioconductor bisulfite-sequencing dmr epigenetics inference methylation
Language:R 54