Bioconductor Workflow Packages

Bioconductor version: Development (3.21)

Package	Maintainer	Title
annotation	Bioconductor Package Maintainer	Genomic Annotation Resources
arrays	Bioconductor Package Maintainer	Using Bioconductor for Microarray Analysis
BiocMetaWorkflow	Mike Smith	BioC Workflow about publishing a Bioc Workflow
BP4RNAseq	Shanwen Sun	A babysitter's package for reproducible RNA-seq analysis
CAGEWorkflow	Malte Thodberg	A step-by-step guide to analyzing CAGE data using R/Bioconductor
chipseqDB	Aaron Lun	A Bioconductor Workflow to Detect Differential Binding in ChIP-seq Data
csawUsersGuide	Aaron Lun	csaw User's Guide
cytofWorkflow	Mark D. Robinson	CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets
EGSEA123	Matthew Ritchie	Easy and efficient ensemble gene set testing with EGSEA
ExpHunterSuite	James Perkins	Package For The Comprehensive Analysis Of Transcriptomic Data
ExpressionNormalizationWorkflow	Karthikeyan Murugesan	Gene Expression Normalization Workflow
fluentGenomics	Stuart Lee	A plyranges and tximeta workflow
generegulation	Bioconductor Package Maintainer	Finding Candidate Binding Sites for Known Transcription Factors via Sequence Matching
GeoMxWorkflows	Maddy Griswold	GeoMx Digital Spatial Profiler (DSP) data analysis workflows
highthroughputassays	Bioconductor Package Maintainer	Using Bioconductor with High Throughput Assays
liftOver	Bioconductor Package Maintainer	Changing genomic coordinate systems with rtracklayer::liftOver
maEndToEnd	Stefanie Reisenauer	An end to end workflow for differential gene expression using Affymetrix microarrays
methylationArrayAnalysis	Jovana Maksimovic	A cross-package Bioconductor workflow for analysing methylation array data.
recountWorkflow	Leonardo Collado-Torres	recount workflow: accessing over 70,000 human RNA-seq samples with Bioconductor
RNAseq123	Matthew Ritchie	RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR
rnaseqDTU	Michael Love	RNA-seq workflow for differential transcript usage following Salmon quantification
rnaseqGene	Michael Love	RNA-seq workflow: gene-level exploratory analysis and differential expression
RnaSeqGeneEdgeRQL	Yunshun Chen	Gene-level RNA-seq differential expression and pathway analysis using Rsubread and the edgeR quasi-likelihood pipeline
seqpac	Daniel Natt	Seqpac: A Framework for smallRNA analysis in R using Sequence-Based Counts
sequencing	Bioconductor Package Maintainer	Introduction to Bioconductor for Sequence Data
simpleSingleCell	Aaron Lun	A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor
SingscoreAMLMutations	Dharmesh D. Bhuva	Using singscore to predict mutations in AML from transcriptomic signatures
spicyWorkflow	SOMS Maintainer	Performing a Spatial Analysis of Multiplexed Tissue Imaging Data
TCGAWorkflow	Tiago Chedraoui Silva	TCGA Workflow Analyze cancer genomics and epigenomics data using Bioconductor packages
variants	Bioconductor Package Maintainer	Annotating Genomic Variants