bioconductor.org "BatchEffect" keyword
View the packages on the bioconductor.org package registry that are tagged with the "BatchEffect" keyword.
roastgsa 1.6.0
Rotation based gene set analysis4 versions - Latest release: 3 months ago - 4.06 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 0.3% on bioconductor.org
14 versions - Latest release: 2 months ago - 322 dependent packages - 5.97 million downloads total - 1 maintainer
limma 3.64.1
Linear Models for Microarray and Omics Data14 versions - Latest release: 2 months ago - 322 dependent packages - 5.97 million downloads total - 1 maintainer
HarmonizR 1.6.0
Handles missing values and makes more data available4 versions - Latest release: 3 months ago - 4.51 thousand downloads total - 1 maintainer
Top 0.6% on bioconductor.org
23 versions - Latest release: 18 days ago - 181 dependent packages - 3.6 million downloads total - 4 maintainers
edgeR 4.6.3
Empirical Analysis of Digital Gene Expression Data in R23 versions - Latest release: 18 days ago - 181 dependent packages - 3.6 million downloads total - 4 maintainers
Top 1.7% on bioconductor.org
6 versions - Latest release: 3 months ago - 43 dependent packages - 965 thousand downloads total - 3 maintainers
sva 3.56.0
Surrogate Variable Analysis6 versions - Latest release: 3 months ago - 43 dependent packages - 965 thousand downloads total - 3 maintainers
crumblr 1.0.0
Count ratio uncertainty modeling base linear regression1 version - Latest release: 3 months ago - 1.15 thousand downloads total - 6 stars on GitHub - 1 maintainer
DegNorm 1.18.0
DegNorm: degradation normalization for RNA-seq data5 versions - Latest release: 2 months ago - 8.5 thousand downloads total - 1 stars on GitHub - 1 maintainer
gemma.R 3.4.5
A wrapper for Gemma's Restful API to access curated gene expression data and differential express...16 versions - Latest release: 9 days ago - 6.41 thousand downloads total - 10 stars on GitHub - 1 maintainer
fishpond 2.14.0
Fishpond: downstream methods and tools for expression data5 versions - Latest release: 2 months ago - 1 dependent package - 36.4 thousand downloads total - 29 stars on GitHub - 1 maintainer
MAGAR 1.16.0
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation an...5 versions - Latest release: 3 months ago - 8.23 thousand downloads total - 0 stars on GitHub - 1 maintainer
NewWave 1.18.0
Negative binomial model for scRNA-seq5 versions - Latest release: 3 months ago - 9.31 thousand downloads total - 4 stars on GitHub - 1 maintainer
ChromSCape 1.17.0
Analysis of single-cell epigenomics datasets with a Shiny App5 versions - Latest release: 2 months ago - 7.92 thousand downloads total - 14 stars on GitHub - 1 maintainer
protGear 1.12.0
Protein Micro Array Data Management and Interactive Visualization5 versions - Latest release: 3 months ago - 7.62 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 2.9% on bioconductor.org
6 versions - Latest release: 3 months ago - 4 dependent packages - 242 thousand downloads total - 1 stars on GitHub - 1 maintainer
ResidualMatrix 1.18.0
Creating a DelayedMatrix of Regression Residuals6 versions - Latest release: 3 months ago - 4 dependent packages - 242 thousand downloads total - 1 stars on GitHub - 1 maintainer
gcapc 1.32.0
GC Aware Peak Caller5 versions - Latest release: 3 months ago - 1 dependent package - 14.3 thousand downloads total - 9 stars on GitHub - 1 maintainer
variancePartition 1.38.0
Quantify and interpret drivers of variation in multilevel gene expression experiments9 versions - Latest release: 3 months ago - 4 dependent packages - 84.2 thousand downloads total - 8 stars on GitHub - 1 maintainer
MethylAid 1.42.0
Visual and interactive quality control of large Illumina DNA Methylation array data sets5 versions - Latest release: 3 months ago - 25.3 thousand downloads total - 1 maintainer
qsmooth 1.24.0
Smooth quantile normalization5 versions - Latest release: 3 months ago - 12.5 thousand downloads total - 1 maintainer
scrapper 1.2.1
Bindings to C++ Libraries for Single-Cell Analysis5 versions - Latest release: about 2 months ago - 4.19 thousand downloads total - 1 maintainer
erccdashboard 1.42.0
Assess Differential Gene Expression Experiments with ERCC Controls5 versions - Latest release: 3 months ago - 24 thousand downloads total - 7 stars on GitHub - 1 maintainer
BERT 1.4.0
High Performance Data Integration for Large-Scale Analyses of Incomplete Omic Profiles Using Batc...3 versions - Latest release: 3 months ago - 3.24 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
5 versions - Latest release: 3 months ago - 49.2 thousand downloads total - 1 maintainer
pvca 1.48.0
Principal Variance Component Analysis (PVCA)5 versions - Latest release: 3 months ago - 49.2 thousand downloads total - 1 maintainer
SurfR 1.4.1
Surface Protein Prediction and Identification8 versions - Latest release: 26 days ago - 3.48 thousand downloads total - 0 stars on GitHub - 1 maintainer
CellMixS 1.24.0
Evaluate Cellspecific Mixing5 versions - Latest release: 3 months ago - 11.8 thousand downloads total - 7 stars on GitHub - 1 maintainer
POMA 1.18.0
Tools for Omics Data Analysis5 versions - Latest release: 3 months ago - 1 dependent package - 10.6 thousand downloads total - 11 stars on GitHub - 1 maintainer
metaseqR2 1.20.0
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statisti...5 versions - Latest release: 3 months ago - 9.37 thousand downloads total - 1 maintainer
OpenStats 1.20.0
A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phen...5 versions - Latest release: 3 months ago - 7.57 thousand downloads total - 1 maintainer
IsoformSwitchAnalyzeR 2.8.0
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- a...5 versions - Latest release: 3 months ago - 37.7 thousand downloads total - 1 maintainer
zenith 1.10.0
Gene set analysis following differential expression using linear (mixed) modeling with dream6 versions - Latest release: 3 months ago - 2 dependent packages - 8.28 thousand downloads total - 0 stars on GitHub - 1 maintainer
Harman 1.36.0
The removal of batch effects from datasets using a PCA and constrained optimisation based technique5 versions - Latest release: 3 months ago - 1 dependent package - 25.9 thousand downloads total - 1 maintainer
Top 3.0% on bioconductor.org
6 versions - Latest release: 3 months ago - 5 dependent packages - 339 thousand downloads total - 1 maintainer
batchelor 1.24.0
Single-Cell Batch Correction Methods6 versions - Latest release: 3 months ago - 5 dependent packages - 339 thousand downloads total - 1 maintainer
BUScorrect 1.26.0
Batch Effects Correction with Unknown Subtypes5 versions - Latest release: 3 months ago - 9.99 thousand downloads total - 1 maintainer
phenomis 1.10.0
Postprocessing and univariate analysis of omics data7 versions - Latest release: 3 months ago - 5.74 thousand downloads total - 1 maintainer
PLSDAbatch 1.4.0
PLSDA-batch3 versions - Latest release: 3 months ago - 3.7 thousand downloads total - 13 stars on GitHub - 1 maintainer
sights 1.34.0
Statistics and dIagnostic Graphs for HTS5 versions - Latest release: 3 months ago - 13.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
BatchQC 2.4.0
Batch Effects Quality Control Software5 versions - Latest release: 3 months ago - 25.5 thousand downloads total - 9 stars on GitHub - 1 maintainer
KnowSeq 1.22.0
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline5 versions - Latest release: 3 months ago - 10.2 thousand downloads total - 1 maintainer
MMUPHin 1.22.0
Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies5 versions - Latest release: 3 months ago - 14.8 thousand downloads total - 1 maintainer
AMARETTO 1.24.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...5 versions - Latest release: 3 months ago - 14.2 thousand downloads total - 1 maintainer
Top 4.7% on bioconductor.org
5 versions - Latest release: 3 months ago - 1 dependent package - 65.6 thousand downloads total - 1 maintainer
RnBeads 2.26.0
RnBeads5 versions - Latest release: 3 months ago - 1 dependent package - 65.6 thousand downloads total - 1 maintainer
crossmeta 1.34.0
Cross Platform Meta-Analysis of Microarray Data5 versions - Latest release: 3 months ago - 1 dependent package - 18.8 thousand downloads total - 3 stars on GitHub - 1 maintainer
Linnorm 2.32.0
Linear model and normality based normalization and transformation method (Linnorm)5 versions - Latest release: 3 months ago - 1 dependent package - 29.5 thousand downloads total - 1 maintainer
MultiBaC 1.18.0
Multiomic Batch effect Correction5 versions - Latest release: 3 months ago - 9.9 thousand downloads total - 1 maintainer
randRotation 1.20.0
Random Rotation Methods for High Dimensional Data with Batch Structure5 versions - Latest release: 3 months ago - 7.27 thousand downloads total - 0 stars on GitHub - 1 maintainer
BUSseq 1.14.0
Batch Effect Correction with Unknow Subtypes for scRNA-seq data5 versions - Latest release: 3 months ago - 6.18 thousand downloads total - 0 stars on GitHub - 1 maintainer
ramwas 1.32.0
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms5 versions - Latest release: 3 months ago - 16.8 thousand downloads total - 1 maintainer
statTarget 1.38.0
Statistical Analysis of Molecular Profiles5 versions - Latest release: 3 months ago - 26.7 thousand downloads total - 1 maintainer
ENmix 1.44.1
Quality control and analysis tools for Illumina DNA methylation BeadChip8 versions - Latest release: 2 months ago - 37.6 thousand downloads total - 1 maintainer
wpm 1.18.0
Well Plate Maker5 versions - Latest release: 3 months ago - 7.78 thousand downloads total - 5 stars on GitHub - 1 maintainer
corral 1.18.0
Correspondence Analysis for Single Cell Data5 versions - Latest release: 3 months ago - 9.22 thousand downloads total - 1 maintainer
pmp 1.20.0
Peak Matrix Processing and signal batch correction for metabolomics datasets6 versions - Latest release: 3 months ago - 2 dependent packages - 12.6 thousand downloads total - 1 maintainer
scBFA 1.22.0
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile...5 versions - Latest release: 3 months ago - 9.33 thousand downloads total - 1 maintainer
scMerge 1.24.0
scMerge: Merging multiple batches of scRNA-seq data5 versions - Latest release: 3 months ago - 2 dependent packages - 33.9 thousand downloads total - 67 stars on GitHub - 1 maintainer
MBECS 1.12.0
Evaluation and correction of batch effects in microbiome data-sets5 versions - Latest release: 3 months ago - 7.57 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 4.8% on bioconductor.org
5 versions - Latest release: 3 months ago - 73.6 thousand downloads total - 1 maintainer
affylmGUI 1.82.0
GUI for limma Package with Affymetrix Microarrays5 versions - Latest release: 3 months ago - 73.6 thousand downloads total - 1 maintainer
singleCellTK 2.18.0
Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data7 versions - Latest release: 3 months ago - 1 dependent package - 26.1 thousand downloads total - 1 maintainer
anota2seq 1.30.0
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq5 versions - Latest release: 3 months ago - 18 thousand downloads total - 2 maintainers
bacon 1.36.0
Controlling bias and inflation in association studies using the empirical null distribution5 versions - Latest release: 3 months ago - 24.8 thousand downloads total - 1 maintainer
iasva 1.26.0
Iteratively Adjusted Surrogate Variable Analysis5 versions - Latest release: 3 months ago - 10.7 thousand downloads total - 2 maintainers
tripr 1.14.0
T-cell Receptor/Immunoglobulin Profiler (TRIP)5 versions - Latest release: 2 months ago - 6.12 thousand downloads total - 2 stars on GitHub - 1 maintainer
dreamlet 1.6.0
Scalable differential expression analysis of single cell transcriptomics datasets with complex st...6 versions - Latest release: 3 months ago - 5.2 thousand downloads total - 12 stars on GitHub - 1 maintainer
seahtrue 1.2.0
Seahtrue revives XF data for structured data analysis2 versions - Latest release: 3 months ago - 1.88 thousand downloads total - 0 stars on GitHub - 1 maintainer
BEclear 2.24.0
Correction of batch effects in DNA methylation data5 versions - Latest release: 3 months ago - 20.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
BatchSVG 1.0.0
Identify Batch-Biased Features in Spatially Variable Genes1 version - Latest release: 3 months ago - 902 downloads total - 2 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
5 versions - Latest release: 3 months ago - 54.2 thousand downloads total - 1 maintainer
limmaGUI 1.84.0
GUI for limma Package With Two Color Microarrays5 versions - Latest release: 3 months ago - 54.2 thousand downloads total - 1 maintainer
proBatch 1.15.1 removed
Tools for Diagnostics and Corrections of Batch Effects in Proteomics1 version - Latest release: almost 2 years ago - 5.93 thousand downloads total - 14 stars on GitHub - 1 maintainer
BDMMAcorrect 1.22.0 removed
Meta-analysis for the metagenomic read counts data from different cohorts3 versions - Latest release: about 1 year ago - 6.75 thousand downloads total - 1 maintainer
alpine 1.26.0 removed
alpine1 version - Latest release: almost 2 years ago - 12.2 thousand downloads total - 1 maintainer
genotypeeval 1.31.1 removed
QA/QC of a gVCF or VCF file1 version - Latest release: almost 2 years ago - 10.4 thousand downloads total - 1 maintainer
Related Keywords
Software
69
Normalization
38
QualityControl
35
GeneExpression
35
Preprocessing
33
Sequencing
28
RNASeq
28
ImmunoOncology
26
DifferentialExpression
26
Microarray
22
Regression
20
Transcriptomics
19
MultipleComparison
18
DataImport
17
Clustering
16
SingleCell
16
Transcription
15
StatisticalMethod
15
Visualization
15
Bayesian
14
Epigenetics
12
PrincipalComponent
11
GeneSetEnrichment
11
FunctionalGenomics
10
AlternativeSplicing
9
DifferentialSplicing
9
DNAMethylation
8
TwoChannel
8
Proteomics
8
SystemsBiology
7
TimeCourse
7
mRNAMicroarray
7
Genetics
7
OneChannel
7
BiomedicalInformatics
7
GUI
6
MethylationArray
6
ExperimentalDesign
6
Coverage
6
Metabolomics
6
DifferentialMethylation
6
FeatureExtraction
5
r
5
DimensionReduction
5
Pathways
5
ChIPSeq
5
ProprietaryPlatforms
5
CellBiology
5
MassSpectrometry
5
Classification
4
Microbiome
4
Annotation
4
bioinformatics
4
MicroRNAArray
4
ATACSeq
3
Alignment
3
DataRepresentation
3
GO
3
batch-effects
3
Network
3
FunctionalPrediction
3
MethylSeq
3
ReportWriting
3
ExonArray
3
bioconductor-package
3
Cheminformatics
3
GeneRegulation
3
bioconductor
3
GenomeWideAssociation
2
shiny
2
single-cell
2
KEGG
2
CellBasedAssays
2
MicrotitrePlateAssay
2
GenePrediction
2
rpackage
2
PeakDetection
2
SNP
2
GraphAndNetwork
2
CpGIsland
2
CopyNumberVariation
2
rstats
2
batch-effect
2
rnaseq
2
transcriptomics
2
genomics
2
VariantAnnotation
1
TranscriptomeVariant
1
WorkflowStep
1
workflow
1
user-friendly
1
statistical-analysis
1
r-package
1
pre-processing
1
pipeline
1
omics-data-integration
1
proteome
1
normalization
1
spatial-transcriptomics
1
Spatial
1