Bioconductor Packages

A babysitter's package for reproducible RNA-seq analysis

R-side access to BioPlex protein-protein interaction data

"Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oleś M, Lu J et al. - experimental data and complete analysis

A step-by-step guide to analyzing CAGE data using R/Bioconductor

Easy and efficient ensemble gene set testing with EGSEA

Package for the Comprehensive Analysis of Transcriptomic Data

Gene Expression Normalization Workflow

Tumor, tumor-adjacent normal, and healthy colorectal transcriptomes as SummarizedExperiment objects

GeoMx Digital Spatial Profiler (DSP) data analysis workflows

16S rRNA Sequencing Data from the Human Microbiome Project

16s rRNA sequencing data from the Human Microbiome Project 2

Processed Harmonized TCGA Data of Five Selected Cancer Types

Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages

Reproduce figures in IHW paper

LegATo: Longitudinal mEtaGenomic Analysis Toolkit

Data package for Multi-Omics Factor Analysis (MOFA)

Tools and functions for preprocessing 16S and metagenomic sequencing microbiome data

Datasets for benchmarking in microbiome research

NestLink an R data package to guide through Engineered Peptide Barcodes for In-Depth Analyzes of Binding Protein Ensembles

Data package for phylogenetic profile analysis using PhyloProfile tool

Programmatic access to ProteinGym datasets in R/Bioconductor

P. tricornutum HPLC-ESI-MS Lipid Data from van Creveld et al. (2015)

RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR

Companion package to the 'Using R and Bioconductor for proteomics data analysis' publication

Gene-level RNA-seq differential expression and pathway analysis using Rsubread and the edgeR quasi-likelihood pipeline

Collection of spatial transcriptomics datasets in SpatialExperiment Bioconductor format

Integrating Multi-modal Single Cell Experiment datasets

Collection of spatial omics datasets

Visium spatial gene expression data by 10X Genomics

Vectra Polaris and Vectra 3 multiplex single-cell imaging data

Spatially-resolved transcriptomics and single-nucleus RNA-sequencing data from the locus coeruleus (LC) in postmortem human brain samples

Using Bioconductor for Microarray Analysis

A harmonized data resource and software for enrichment analysis of microbial physiologies

ExperimentHub data for the cfTools package

Curated Metagenomic Data of the Human Microbiome

Curated Prostate Cancer Data

Curated Data from The Cancer Genome Atlas (TCGA) as MultiAssayExperiment Objects

Data and analysis scripts for David, Huber et al. yeast tiling array paper

Cancer Dependency Map Data Package

easier internal data and exemplary dataset from IMvigor210CoreBiologies package

A plyranges and tximeta workflow

Furrow Segmentation

an R package for visualization of tree and annotation data

Unknown annotation data (chip hguDKFZ31)

Unknown annotation data (chip hgubeta7)

Collection of publicly available imaging mass cytometry (IMC) datasets

Changing genomic coordinate systems with rtracklayer::liftOver

An end to end workflow for differential gene expression using Affymetrix microarrays

Sigma mix MSQC1 data

RNA-seq workflow for differential transcript usage following Salmon quantification