bioconductor.org "BatchEffect" keyword
Top 0.6% on bioconductor.org
26 versions - Latest release: 2 months ago - 181 dependent packages - 4.28 million downloads total - 4 maintainers
edgeR 4.8.2
Empirical Analysis of Digital Gene Expression Data in R26 versions - Latest release: 2 months ago - 181 dependent packages - 4.28 million downloads total - 4 maintainers
Top 1.7% on bioconductor.org
7 versions - Latest release: 4 months ago - 43 dependent packages - 1.18 million downloads total - 3 maintainers
sva 3.58.0
Surrogate Variable Analysis7 versions - Latest release: 4 months ago - 43 dependent packages - 1.18 million downloads total - 3 maintainers
Top 0.3% on bioconductor.org
16 versions - Latest release: 4 months ago - 322 dependent packages - 6.97 million downloads total - 1 maintainer
limma 3.66.0
Linear Models for Microarray and Omics Data16 versions - Latest release: 4 months ago - 322 dependent packages - 6.97 million downloads total - 1 maintainer
notame 1.0.1
Workflow for non-targeted LC-MS metabolic profiling2 versions - Latest release: about 2 months ago - 1.54 thousand downloads total - 3 stars on GitHub - 1 maintainer
Coralysis 1.0.0
Coralysis sensitive identification of imbalanced cell types and states in single-cell data via mu...1 version - Latest release: 4 months ago - 1.96 thousand downloads total - 1 stars on GitHub - 1 maintainer
MetaDICT 1.0.0
Microbiome data integration method via shared dictionary learning1 version - Latest release: 4 months ago - 933 downloads total - 2 stars on GitHub - 1 maintainer
scrapper 1.4.0
Bindings to C++ Libraries for Single-Cell Analysis6 versions - Latest release: 3 months ago - 19.1 thousand downloads total - 1 maintainer
bacon 1.38.0
Controlling bias and inflation in association studies using the empirical null distribution6 versions - Latest release: 3 months ago - 30.3 thousand downloads total - 1 maintainer
randRotation 1.22.0
Random Rotation Methods for High Dimensional Data with Batch Structure6 versions - Latest release: 4 months ago - 9.43 thousand downloads total - 0 stars on GitHub - 1 maintainer
Harman 1.38.0
The removal of batch effects from datasets using a PCA and constrained optimisation based technique6 versions - Latest release: 3 months ago - 1 dependent package - 31 thousand downloads total - 1 maintainer
roastgsa 1.8.0
Rotation based gene set analysis5 versions - Latest release: 3 months ago - 5.83 thousand downloads total - 0 stars on GitHub - 1 maintainer
OpenStats 1.22.0
A Robust and Scalable Software Package for Reproducible Analysis of High-Throughput genotype-phen...6 versions - Latest release: 3 months ago - 9.71 thousand downloads total - 1 maintainer
zenith 1.12.0
Gene set analysis following differential expression using linear (mixed) modeling with dream7 versions - Latest release: 3 months ago - 2 dependent packages - 12.2 thousand downloads total - 0 stars on GitHub - 1 maintainer
HarmonizR 1.8.0
Handles missing values and makes more data available5 versions - Latest release: 3 months ago - 6.79 thousand downloads total - 1 maintainer
crumblr 1.2.0
Count ratio uncertainty modeling base linear regression2 versions - Latest release: 4 months ago - 2.78 thousand downloads total - 6 stars on GitHub - 1 maintainer
MMUPHin 1.24.0
Meta-analysis Methods with Uniform Pipeline for Heterogeneity in Microbiome Studies7 versions - Latest release: about 1 month ago - 18.1 thousand downloads total - 1 maintainer
batchCorr 1.0.0
Within And Between Batch Correction Of LC-MS Metabolomics Data1 version - Latest release: 4 months ago - 1.41 thousand downloads total - 0 stars on GitHub - 1 maintainer
scBFA 1.24.0
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile...6 versions - Latest release: 4 months ago - 11.9 thousand downloads total - 1 maintainer
Top 5.4% on bioconductor.org
6 versions - Latest release: 3 months ago - 58 thousand downloads total - 1 maintainer
limmaGUI 1.86.0
GUI for limma Package With Two Color Microarrays6 versions - Latest release: 3 months ago - 58 thousand downloads total - 1 maintainer
BUSseq 1.16.0
Batch Effect Correction with Unknow Subtypes for scRNA-seq data6 versions - Latest release: 4 months ago - 9.24 thousand downloads total - 0 stars on GitHub - 1 maintainer
iasva 1.28.0
Iteratively Adjusted Surrogate Variable Analysis6 versions - Latest release: 3 months ago - 14.2 thousand downloads total - 2 maintainers
dreamlet 1.8.0
Scalable differential expression analysis of single cell transcriptomics datasets with complex st...7 versions - Latest release: 4 months ago - 9.48 thousand downloads total - 20 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
6 versions - Latest release: 3 months ago - 1 dependent package - 80.7 thousand downloads total - 1 maintainer
RnBeads 2.28.0
RnBeads6 versions - Latest release: 3 months ago - 1 dependent package - 80.7 thousand downloads total - 1 maintainer
Top 2.9% on bioconductor.org
7 versions - Latest release: 4 months ago - 4 dependent packages - 344 thousand downloads total - 1 stars on GitHub - 1 maintainer
ResidualMatrix 1.20.0
Creating a DelayedMatrix of Regression Residuals7 versions - Latest release: 4 months ago - 4 dependent packages - 344 thousand downloads total - 1 stars on GitHub - 1 maintainer
ramwas 1.34.0
Fast Methylome-Wide Association Study Pipeline for Enrichment Platforms6 versions - Latest release: 3 months ago - 21 thousand downloads total - 1 maintainer
BUScorrect 1.28.0
Batch Effects Correction with Unknown Subtypes6 versions - Latest release: 3 months ago - 12.8 thousand downloads total - 1 maintainer
NewWave 1.20.0
Negative binomial model for scRNA-seq6 versions - Latest release: 3 months ago - 11.9 thousand downloads total - 4 stars on GitHub - 1 maintainer
IsoformSwitchAnalyzeR 2.10.0
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- a...6 versions - Latest release: 3 months ago - 50.4 thousand downloads total - 1 maintainer
AMARETTO 1.26.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...6 versions - Latest release: 4 months ago - 17.2 thousand downloads total - 1 maintainer
Top 4.8% on bioconductor.org
6 versions - Latest release: 3 months ago - 78.5 thousand downloads total - 1 maintainer
affylmGUI 1.84.0
GUI for limma Package with Affymetrix Microarrays6 versions - Latest release: 3 months ago - 78.5 thousand downloads total - 1 maintainer
ENmix 1.46.1
Quality control and analysis tools for Illumina DNA methylation BeadChip11 versions - Latest release: about 1 month ago - 48.8 thousand downloads total - 1 maintainer
Top 3.0% on bioconductor.org
7 versions - Latest release: 3 months ago - 5 dependent packages - 444 thousand downloads total - 1 maintainer
batchelor 1.26.0
Single-Cell Batch Correction Methods7 versions - Latest release: 3 months ago - 5 dependent packages - 444 thousand downloads total - 1 maintainer
DegNorm 1.20.0
DegNorm: degradation normalization for RNA-seq data6 versions - Latest release: 3 months ago - 11.1 thousand downloads total - 1 stars on GitHub - 1 maintainer
qsmooth 1.26.0
Smooth quantile normalization6 versions - Latest release: 3 months ago - 16.1 thousand downloads total - 1 maintainer
cellmig 1.0.0
Uncertainty-aware quantitative analysis of high-throughput live cell migration data2 versions - Latest release: 3 months ago - 1.16 thousand downloads total - 1 stars on GitHub - 1 maintainer
anota2seq 1.32.0
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq6 versions - Latest release: 3 months ago - 23.1 thousand downloads total - 2 maintainers
corral 1.20.0
Correspondence Analysis for Single Cell Data6 versions - Latest release: 3 months ago - 12 thousand downloads total - 1 maintainer
singleCellTK 2.20.1
Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data11 versions - Latest release: about 1 month ago - 1 dependent package - 39.2 thousand downloads total - 1 maintainer
sights 1.36.0
Statistics and dIagnostic Graphs for HTS6 versions - Latest release: 4 months ago - 16.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
anglemania 1.0.0
Feature Extraction for scRNA-seq Dataset Integration1 version - Latest release: 4 months ago - 1.01 thousand downloads total - 4 stars on GitHub - 1 maintainer
pmp 1.22.1
Peak Matrix Processing and signal batch correction for metabolomics datasets7 versions - Latest release: 4 months ago - 2 dependent packages - 16.9 thousand downloads total - 1 maintainer
BatchSVG 1.2.0
Identify Batch-Biased Features in Spatially Variable Genes2 versions - Latest release: 4 months ago - 2.83 thousand downloads total - 3 stars on GitHub - 1 maintainer
erccdashboard 1.44.0
Assess Differential Gene Expression Experiments with ERCC Controls6 versions - Latest release: 4 months ago - 27 thousand downloads total - 7 stars on GitHub - 1 maintainer
SmartPhos 1.0.0
A phosphoproteomics data analysis package with an interactive ShinyApp1 version - Latest release: 4 months ago - 339 downloads total - 5 stars on GitHub - 1 maintainer
Linnorm 2.34.0
Linear model and normality based normalization and transformation method (Linnorm)6 versions - Latest release: 4 months ago - 1 dependent package - 35.3 thousand downloads total - 1 maintainer
CellMixS 1.26.0
Evaluate Cellspecific Mixing6 versions - Latest release: 3 months ago - 18 thousand downloads total - 7 stars on GitHub - 1 maintainer
proBatch 1.15.1 removed
Tools for Diagnostics and Corrections of Batch Effects in Proteomics1 version - Latest release: over 2 years ago - 5.93 thousand downloads total - 17 stars on GitHub - 1 maintainer
PLSDAbatch 1.6.0
PLSDA-batch4 versions - Latest release: 4 months ago - 5.5 thousand downloads total - 13 stars on GitHub - 1 maintainer
tripr 1.16.0
T-cell Receptor/Immunoglobulin Profiler (TRIP)6 versions - Latest release: 4 months ago - 8.49 thousand downloads total - 2 stars on GitHub - 1 maintainer
gcapc 1.34.0
GC Aware Peak Caller6 versions - Latest release: 3 months ago - 1 dependent package - 17.6 thousand downloads total - 9 stars on GitHub - 1 maintainer
statTarget 1.40.0
Statistical Analysis of Molecular Profiles6 versions - Latest release: 3 months ago - 31.1 thousand downloads total - 1 maintainer
BEclear 2.26.0
Correction of batch effects in DNA methylation data6 versions - Latest release: 3 months ago - 23.7 thousand downloads total - 5 stars on GitHub - 1 maintainer
BatchQC 2.6.1
Batch Effects Quality Control Software7 versions - Latest release: 19 days ago - 29.7 thousand downloads total - 9 stars on GitHub - 1 maintainer
gemma.R 3.6.1
A wrapper for Gemma's Restful API to access curated gene expression data and differential express...18 versions - Latest release: about 1 month ago - 9.03 thousand downloads total - 10 stars on GitHub - 1 maintainer
MBECS 1.14.0
Evaluation and correction of batch effects in microbiome data-sets6 versions - Latest release: 3 months ago - 9.98 thousand downloads total - 4 stars on GitHub - 1 maintainer
SurfR 1.6.0
Surface Protein Prediction and Identification10 versions - Latest release: 4 months ago - 5.41 thousand downloads total - 0 stars on GitHub - 1 maintainer
MAGAR 1.18.0
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation an...6 versions - Latest release: 3 months ago - 10.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
notameViz 1.0.2
Workflow for non-targeted LC-MS metabolic profiling2 versions - Latest release: 20 days ago - 1.08 thousand downloads total - 0 stars on GitHub - 1 maintainer
BERT 1.6.0
High Performance Data Integration for Large-Scale Analyses of Incomplete Omic Profiles Using Batc...4 versions - Latest release: 4 months ago - 4.9 thousand downloads total - 4 stars on GitHub - 1 maintainer
seahtrue 1.4.0
Seahtrue revives XF data for structured data analysis3 versions - Latest release: 3 months ago - 3.93 thousand downloads total - 0 stars on GitHub - 1 maintainer
scMerge 1.26.0
scMerge: Merging multiple batches of scRNA-seq data6 versions - Latest release: 4 months ago - 2 dependent packages - 49.7 thousand downloads total - 68 stars on GitHub - 1 maintainer
metaseqR2 1.22.0
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statisti...6 versions - Latest release: 3 months ago - 12.2 thousand downloads total - 1 maintainer
wpm 1.20.0
Well Plate Maker6 versions - Latest release: 4 months ago - 10.1 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 6.1% on bioconductor.org
6 versions - Latest release: 4 months ago - 59.6 thousand downloads total - 1 maintainer
pvca 1.50.0
Principal Variance Component Analysis (PVCA)6 versions - Latest release: 4 months ago - 59.6 thousand downloads total - 1 maintainer
protGear 1.14.0
Protein Micro Array Data Management and Interactive Visualization6 versions - Latest release: 4 months ago - 9.72 thousand downloads total - 1 stars on GitHub - 1 maintainer
KnowSeq 1.24.0
KnowSeq R/Bioc package: The Smart Transcriptomic Pipeline6 versions - Latest release: 3 months ago - 13.8 thousand downloads total - 1 maintainer
phenomis 1.12.0
Postprocessing and univariate analysis of omics data8 versions - Latest release: 3 months ago - 7.53 thousand downloads total - 1 maintainer
ChromSCape 1.20.0
Analysis of single-cell epigenomics datasets with a Shiny App6 versions - Latest release: 4 months ago - 10.2 thousand downloads total - 14 stars on GitHub - 1 maintainer
notameStats 1.0.0
Workflow for non-targeted LC-MS metabolic profiling1 version - Latest release: 4 months ago - 586 downloads total - 0 stars on GitHub - 1 maintainer
variancePartition 1.40.1
Quantify and interpret drivers of variation in multilevel gene expression experiments12 versions - Latest release: 2 months ago - 4 dependent packages - 131 thousand downloads total - 10 stars on GitHub - 1 maintainer
fishpond 2.16.0
Fishpond: downstream methods and tools for expression data6 versions - Latest release: 3 months ago - 1 dependent package - 58.8 thousand downloads total - 29 stars on GitHub - 1 maintainer
POMA 1.20.0
Tools for Omics Data Analysis6 versions - Latest release: 4 months ago - 1 dependent package - 15.1 thousand downloads total - 12 stars on GitHub - 1 maintainer
MultiBaC 1.20.0
Multiomic Batch effect Correction6 versions - Latest release: 3 months ago - 12.3 thousand downloads total - 1 maintainer
MethylAid 1.44.0
Visual and interactive quality control of large Illumina DNA Methylation array data sets6 versions - Latest release: 4 months ago - 28.2 thousand downloads total - 1 maintainer
HVP 1.0.0
Hierarchical Variance Partitioning1 version - Latest release: 4 months ago - 1.38 thousand downloads total - 1 maintainer
crossmeta 1.34.0 removed
Cross Platform Meta-Analysis of Microarray Data5 versions - Latest release: 11 months ago - 1 dependent package - 19.4 thousand downloads total - 3 stars on GitHub - 1 maintainer
BDMMAcorrect 1.22.0 removed
Meta-analysis for the metagenomic read counts data from different cohorts3 versions - Latest release: almost 2 years ago - 6.75 thousand downloads total - 1 maintainer
alpine 1.26.0 removed
alpine1 version - Latest release: over 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: over 2 years ago - 10.4 thousand downloads total - 1 maintainer
Related Keywords
Software
79
Normalization
43
QualityControl
40
GeneExpression
38
Preprocessing
37
Sequencing
29
RNASeq
29
DifferentialExpression
28
ImmunoOncology
26
Microarray
22
MultipleComparison
22
Regression
21
Transcriptomics
21
Clustering
20
DataImport
20
SingleCell
20
Visualization
19
Transcription
15
StatisticalMethod
15
Bayesian
15
GeneSetEnrichment
12
Epigenetics
12
BiomedicalInformatics
11
PrincipalComponent
11
Proteomics
10
FunctionalGenomics
10
Metabolomics
10
MassSpectrometry
10
DifferentialSplicing
9
AlternativeSplicing
9
DNAMethylation
8
TwoChannel
8
SystemsBiology
7
TimeCourse
7
ExperimentalDesign
7
GUI
7
Genetics
7
mRNAMicroarray
7
OneChannel
7
DimensionReduction
6
CellBiology
6
FeatureExtraction
6
Coverage
6
MethylationArray
6
DifferentialMethylation
6
Microbiome
5
r
5
Classification
5
Annotation
5
Pathways
5
ChIPSeq
5
ProprietaryPlatforms
5
MicroRNAArray
4
bioinformatics
4
MethylSeq
3
GO
3
DataRepresentation
3
batch-effects
3
ReportWriting
3
FunctionalPrediction
3
Network
3
Alignment
3
bioconductor-package
3
bioconductor
3
GeneRegulation
3
ATACSeq
3
ExonArray
3
Cheminformatics
3
shiny
2
rpackage
2
GraphAndNetwork
2
genomics
2
data-integration
2
transcriptomics
2
PeakDetection
2
ShinyApps
2
batch-effect
2
single-cell
2
MicrotitrePlateAssay
2
CellBasedAssays
2
scrna-seq
2
rstats
2
CpGIsland
2
GenomeWideAssociation
2
CopyNumberVariation
2
KEGG
2
GenePrediction
2
rnaseq
2
SNP
2
statistical-analysis
1
proteomics-data
1
GeneticVariability
1
normalisation
1
microarray-data
1
data-science
1
nature-communications
1
VariantAnnotation
1
background-correction
1
WorkflowStep
1
r-package
1