Bioconductor Topics

Microarray QA and statistical data analysis for Applied Biosystems Genome Survey Microrarray (AB1700) gene expression data.

Algorithms for Calculating Microarray Enrichment (ACME)

ADAM: Activity and Diversity Analysis Module

Analysis of Big Data from aCGH Experiments using Parallel Computing and ff Objects

Agreement of Differential Expression Analysis

AIMS : Absolute Assignment of Breast Cancer Intrinsic Molecular Subtype

Active modules for multilayer weighted gene co-expression networks: a continuous optimization approach

Adaptive Robust Regression normalization for Illumina methylation data

Analyze and correct probe positional bias in microarray data due to RNA degradation

Processing and Differential Expression Analysis of Agilent microRNA chips

Manipulation of SQLite-based annotations in Bioconductor

Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet

BLMA: A package for bi-level meta-analysis

Batch Effects Quality Control Software

Compression of Illumina BeadArray data

Annotation and gene expression data retrieval from Bgee database. TopAnat, an anatomical entities Enrichment Analysis tool for UBERON ontology

Biclustering Analysis and Results Exploration

Routines for the functional analysis of biological networks

Chromosmal Aberrations Finder in Expression data

PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data

Co-expression Modules identification Tool

CGHbase: Base functions and classes for arrayCGH data analysis.

Normalization of array CGH data with imbalanced aberrations.

Dimension Reduction for Array CGH Data with Minimal Information Loss.

Convert segment data into a region by sample matrix to allow for other high level computational analyses.

Summarization and expression/phenotype association of CNV ranges

Coordinate Covariation Analysis

Candidate Driver Analysis

Causal network analysis methods

Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

Predict genes expressed selectively in specific cell types

Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC

ChIPanalyser: Predicting Transcription Factor Binding Sites

Coordinated Gene Activity in Pattern Sets

Create Copy-Number Plots using karyoploteR functionality

Correlation Motif Fit

Tools for curating, analyzing, and manipulating biological sequences

Two-sample tests on a graph

Gene Selection

Methylation array and sequencing spatial analysis methods

DNA Copy Number Data Analysis

Dynamic Transcriptome Analysis

Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms

Comparison of disease and drug profiles using Gene set Enrichment Analysis

Ensemble of Gene Set Enrichment Analyses

Earth Mover's Distance for Differential Analysis of Genomics Data

Quality control and analysis tools for Illumina DNA methylation BeadChip

Expression Weighted Celltype Enrichment

Predicting Disease Progression Based on Methylation Correlated Blocks using Ensemble Models

Seamless navigation through combined results of set-based and network-based enrichment analysis