Bioconductor Workflow Packages

Bioconductor version: Release (3.10)

Package Maintainer Title
annotation Bioconductor Package Maintainer Genomic Annotation Resources
arrays Bioconductor Package Maintainer Using Bioconductor for Microarray Analysis
BgeeCall Julien Wollbrett BgeeCall, a R package for automatic RNA-Seq present/absent gene expression calls generation
BiocMetaWorkflow Mike Smith BioC Workflow about publishing a Bioc Workflow
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 Malgorzata Nowicka CyTOF workflow: differential discovery in high-throughput high-dimensional cytometry datasets
EGSEA123 Matthew Ritchie Easy and efficient ensemble gene set testing with EGSEA
eQTL Vincent Carey Cloud-enabled cis-eQTL searches with Bioconductor GGtools 5.x
ExpressionNormalizationWorkflow Karthikeyan Murugesan Gene Expression Normalization Workflow
generegulation Bioconductor Package Maintainer Finding Candidate Binding Sites for Known Transcription Factors via Sequence Matching
highthroughputassays Bioconductor Package Maintainer Using Bioconductor with High Throughput Assays
liftOver Bioconductor Package Maintainer Changing genomic coordinate systems with rtracklayer::liftOver
maEndToEnd Bernd Klaus 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.
proteomics Laurent Gatto Mass spectrometry and proteomics data analysis
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
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
TCGAWorkflow Tiago Chedraoui Silva TCGA Workflow Analyze cancer genomics and epigenomics data using Bioconductor packages
variants Bioconductor Package Maintainer Annotating Genomic Variants

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