Biocview "BatchEffect"

A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq

Adjust for positional and batch effects using ComBat

alpine

Analysis of single-cell epigenomics datasets with a Shiny App

An Interactive Consensus Clustering Framework for Multi-platform Data Analysis

An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms

A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phenotype association

ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression

Assess Differential Gene Expression Experiments with ERCC Controls

Association analysis of CNVs and imputed SNPs incorporating uncertainty

A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

Batch Effects Correction with Unknown Subtypes

Batch Effects Quality Control Software

Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Confounding Explorer

Controlling bias and inflation in association studies using the empirical null distribution

Correction of batch effects in DNA methylation data

Correspondence Analysis for Single Cell Data

Creating a DelayedMatrix of Regression Residuals

Cross Platform Meta-Analysis of Microarray Data

Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip

Data preprocessing and quality control for Illumina HumanMethylation450 and MethylationEPIC BeadChip (USC version)

DegNorm: degradation normalization for RNA-seq data

Detecting hidden batch factors through data adaptive adjustment for biological effects

Empirical Analysis of Digital Gene Expression Data in R

Evaluate Cellspecific Mixing

Evaluation and correction of batch effects in microbiome data-sets

Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms

Fishpond: differential transcript and gene expression with inferential replicates

Fishpond: downstream methods and tools for expression data

GC Aware Peak Caller

Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq

Gene set analysis accounting for gene-gene correlations

Gene set analysis following differential expression using linear (mixed) modeling with dream

GUI for limma Package with Affymetrix Microarrays

GUI for limma Package With Two Color Microarrays

Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.

Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

ImagingAMARETTO: tools for interpreting multi-omics networks for relevance to clinical outcomes and radiographic and histopathology imaging-derived biomarkers

Iteratively Adjusted Surrogate Variable Analysis

k-nearest neighbour batch effect test

KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline

Linear model and normality based normalization and transformation method (Linnorm)

Linear Models for Microarray Data

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

Meta-analysis for the metagenomic read counts data from different cohorts

Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies

Methods for Single-Cell RNA-Seq Data Analysis

Microarray Analysis of Differential Expression

Multiomic Batch effect Correction

Multivariate Information Criteria to identify important predictors in high dimensional multivariate regression

Negative binomial model for scRNA-seq

Peak Matrix Processing and signal batch correction for metabolomics datasets

PLSDA-batch

Principal Variance Component Analysis (PVCA)

Protein Micro Array Data Management and Interactive Visualization

QA/QC of a gVCF or VCF file

Quality control and analysis tools for Illumina DNA methylation BeadChip

Quality Control of Normalized Gene Expression Data

Quantify and interpret divers of variation in multilevel gene expression experiments

Quantify and interpret drivers of variation in multilevel gene expression experiments

Random Rotation Methods for High Dimensional Data with Batch Structure

Rcpp Integration Surrogate Variable Analysis

Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis and Penalized Regression

RnBeads

Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs

scMerge: Merging multiple batches of scRNA-seq data

Single-Cell Batch Correction Methods

Smooth quantile normalization

Statistical Analysis of Molecular Profiles

Statistics and dIagnostic Graphs for HTS

Surrogate Variable Analysis

SVAPLSseq-An R package to estimate the hidden factors of unwanted variability and adjust for them to enable a more powerful and accurate differential expression analysis based on RNAseq data

T-cell Receptor/Immunoglobulin Profiler (TRIP)

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

Tools for Diagnostics and Corrections of Batch Effects in Proteomics

Tools for Omics Data Analysis

Visual and interactive quality control of large Illumina DNA Methylation array data sets

Well Plate Maker

What the Package Does (One Line, Title Case)

Biocview "BatchEffect"

R Package Documentation

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