Bioconductor Topics

Epigenetic Dissection of Intra-Sample-Heterogeneity

An effective identification of alternative splicing events using junction arrays and RNA-Seq data

R functions for the normalization of Exiqon miRNA array data

Representing GDS files as array-like objects

GEM: fast association study for the interplay of Gene, Environment and Methylation

GEOexplorer: a webserver for gene expression analysis and visualisation

Get data from NCBI Gene Expression Omnibus (GEO)

Prepares microarray data for submission to GEO

Gain and Loss Analysis of DNA

Visualise microarray and RNAseq data using gene ontology annotations

Tools for manipulating GO and microarrays

Reproducible GSEA Benchmarking

Linear Model Toolset for Gene Set Enrichment Analysis

Gene Set Regulation Index

Gene Set Variation Analysis for Microarray and RNA-Seq Data

Tools for Genome Wide Association Studies

Pipeline for augmented co-expression analysis

MetaAnalysis for High Throughput Experiments

GeneNetworkBuilder: a bioconductor package for building regulatory network using ChIP-chip/ChIP-seq data and Gene Expression Data

GeneRegionScan

Processing Various Types of Data on GEO and TCGA

NanoString GeoMx Tools

Interactive visualizations for gene expression analysis

Global test for groups of variables via model comparisons

Plotting data and annotation information along genomic coordinates

Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Transposable Data (HDTD)

Tools for HELP data analysis

Heterogeneous error model for identification of differentially expressed genes under multiple conditions

Hierarchical Epitope pROtein biNding

Copy number prediction with correction for GC and mappability bias for HTS data

The removal of batch effects from datasets using a PCA and constrained optimisation based technique

Heatmaps with row and/or column covariates and colored clusters

Hybrid Multiple Testing

ITALICS

Predicting Targets for Drosophila Intragenic miRNAs

Multi sample aCGH analysis package using kernel convolution

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

Methods for analyzing microarray data using Local Pooled Error (LPE) method

Detection of scatterplots with L-shaped pattern

LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for Robust Differential Expression Analysis

MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation and genotyping data

CGH Micro-Array NORmalization

Model-based analysis of DNA methylation data

MBCB (Model-based Background Correction for Beadarray)

Massive correlating biclusters for gene expression data and associated methods

Perform methylation analysis

Muscle Epigenetic Age Test

DNA IP-seq data analysis

Modelling Experimental Data from MeDIP Enrichment

Marker Gene Finder in Microarray gene expression data