Main logo
?
tutorial arrow
×
Submit new tools
Share tools covering the current topic. Provide easy-to-follow guidelines to improve their usability.
Share new tools with the community
Sign up for free to promote the availability of bioinformatics tools

Batch effect correction software tools | RNA sequencing data analysis

It is now known that unwanted noise and unmodeled artifacts such as batch effects can dramatically reduce the accuracy of statistical inference in genomic experiments. These sources of noise must be modeled and removed to accurately measure…
sva
Desktop

sva Surrogate Variable Analysis

Allows to remove batch effects and other unwanted variation in high-throughput…

Allows to remove batch effects and other unwanted variation in high-throughput experiment. SVA is a package containing several functions permitting to identify and build surrogate variables for large…

G T A T C G C T A
AltAnalyze
Desktop

AltAnalyze

An easy-to-use application for microarray, RNA-Seq and metabolomics analysis.…

An easy-to-use application for microarray, RNA-Seq and metabolomics analysis. For splicing sensitive platforms (RNA-Seq or Affymetrix Exon, Gene and Junction arrays), AltAnalyze will assess…

limma
Desktop

limma Linear Models for Microarray Data

Provides an integrated solution for analysing data from gene expression…

Provides an integrated solution for analysing data from gene expression experiments. limma contains rich features for handling complex experimental designs and for information borrowing to overcome…

G T A T C G C T A
gPCA
Desktop

gPCA guided Principal Component Analysis

Provides guided principal components (PCA) analysis for the detection of batch…

Provides guided principal components (PCA) analysis for the detection of batch effects in high-throughput data. gPCA provides a statistic method particularly useful to test whether batch effects…

G T A T C G C T A
svaseq
Desktop

svaseq

Uses surrogate variable analysis (sva) for estimating unwanted noise and…

Uses surrogate variable analysis (sva) for estimating unwanted noise and unmodeled artifacts by (i) identifying the part of the genomic data only affected by artifacts and (ii) estimating the…

G T A T C G C T A
exploBATCH
Desktop

exploBATCH

Evaluates or diagnoses batch effect(s) in genomic data at the level of…

Evaluates or diagnoses batch effect(s) in genomic data at the level of individual principal components (PCs). exploBATCH is a batch evaluation and correction approach based on probabilistic principal…

ComBat
Desktop

ComBat

Adjusting batch effects in microarray expression data using Empirical Bayes…

Adjusting batch effects in microarray expression data using Empirical Bayes methods. The modified ComBat (M-Combat) is designed specifically in the context of meta-analysis and batch effect…

G T A T C G C T A
DASC
Desktop

DASC

Identifies batches in high-dimensional dataset. DASC is able to detect hidden…

Identifies batches in high-dimensional dataset. DASC is able to detect hidden batch factors through data adaptive adjustment for biological effects.

G T A T C G C T A
Fitnoise
Desktop

Fitnoise

Allows users to perform Empirical Bayesian linear modelling. Fitnoise…

Allows users to perform Empirical Bayesian linear modelling. Fitnoise authorizes to experiment measurements related with genes or genomic features by deducing differential expression testing. The…

Information

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.