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bioconductor.org "Microarray" keyword

View the packages on the bioconductor.org package registry that are tagged with the "Microarray" keyword.

Top 1.3% on bioconductor.org
impute 1.82.0
impute: Imputation for microarray data
5 versions - Latest release: 5 months ago - 44 dependent packages - 1.77 million downloads total - 1 maintainer
Top 1.9% on bioconductor.org
minfi 1.54.1
Analyze Illumina Infinium DNA methylation arrays
7 versions - Latest release: 4 months ago - 31 dependent packages - 868 thousand downloads total - 61 stars on GitHub - 1 maintainer
Top 1.7% on bioconductor.org
sva 3.56.0
Surrogate Variable Analysis
6 versions - Latest release: 5 months ago - 43 dependent packages - 999 thousand downloads total - 3 maintainers
Top 2.7% on bioconductor.org
Gviz 1.52.0
Plotting data and annotation information along genomic coordinates
6 versions - Latest release: 4 months ago - 57 dependent packages - 933 thousand downloads total - 86 stars on GitHub - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.64.3
Linear Models for Microarray and Omics Data
15 versions - Latest release: about 1 month ago - 322 dependent packages - 6.25 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
GEOquery 2.76.0
Get data from NCBI Gene Expression Omnibus (GEO)
5 versions - Latest release: 5 months ago - 47 dependent packages - 2.14 million downloads total - 98 stars on GitHub - 1 maintainer
Top 1.8% on bioconductor.org
lumi 2.60.0
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
5 versions - Latest release: 5 months ago - 10 dependent packages - 372 thousand downloads total - 1 maintainer
Top 7.9% on bioconductor.org
BicARE 1.66.0
Biclustering Analysis and Results Exploration
5 versions - Latest release: 4 months ago - 1 dependent package - 49.2 thousand downloads total - 1 maintainer
Top 9.5% on bioconductor.org
genoCN 1.59.0
genotyping and copy number study tools
5 versions - Latest release: 4 months ago - 29.6 thousand downloads total - 1 maintainer
Top 1.7% on bioconductor.org
vsn 3.76.0
Variance stabilization and calibration for microarray data
5 versions - Latest release: 5 months ago - 30 dependent packages - 1.04 million downloads total - 1 maintainer
Top 3.2% on bioconductor.org
oligo 1.72.0
Preprocessing tools for oligonucleotide arrays
7 versions - Latest release: 4 months ago - 11 dependent packages - 451 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 0.7% on bioconductor.org
genefilter 1.90.0
genefilter: methods for filtering genes from high-throughput experiments
5 versions - Latest release: 5 months ago - 66 dependent packages - 3.79 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
multtest 2.64.0
Resampling-based multiple hypothesis testing
5 versions - Latest release: 5 months ago - 37 dependent packages - 2.37 million downloads total - 1 maintainer
BioNetStat 1.24.0 removed
Biological Network Analysis
3 versions - Latest release: over 1 year ago - 9.35 thousand downloads total - 7 stars on GitHub - 1 maintainer
Top 0.9% on bioconductor.org
affy 1.86.0
Methods for Affymetrix Oligonucleotide Arrays
5 versions - Latest release: 5 months ago - 74 dependent packages - 2.08 million downloads total - 1 maintainer
scPCA 1.22.0
Sparse Contrastive Principal Component Analysis
5 versions - Latest release: 5 months ago - 12 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 8.5% on bioconductor.org
geneRecommender 1.80.0
A gene recommender algorithm to identify genes coexpressed with a query set of genes
5 versions - Latest release: 4 months ago - 36.4 thousand downloads total - 1 maintainer
CellMapper 1.34.0
Predict genes expressed selectively in specific cell types
5 versions - Latest release: 4 months ago - 1 maintainer
sigFeature 1.26.0
sigFeature: Significant feature selection using SVM-RFE & t-statistic
5 versions - Latest release: 4 months ago - 1 maintainer
RTopper 1.54.0
This package is designed to perform Gene Set Analysis across multiple genomic platforms
5 versions - Latest release: 4 months ago - 1 maintainer
GOexpress 1.42.0
Visualise microarray and RNAseq data using gene ontology annotations
5 versions - Latest release: 4 months ago - 1 dependent package - 29.8 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 4.6% on bioconductor.org
qpgraph 2.42.0
Estimation of Genetic and Molecular Regulatory Networks from High-Throughput Genomics Data
5 versions - Latest release: 4 months ago - 1 dependent package - 62.4 thousand downloads total - 3 stars on GitHub - 1 maintainer
CINdex 1.36.0
Chromosome Instability Index
5 versions - Latest release: 4 months ago - 16.6 thousand downloads total - 1 maintainer
Top 8.0% on bioconductor.org
OLIN 1.86.0
Optimized local intensity-dependent normalisation of two-color microarrays
5 versions - Latest release: 4 months ago - 2 dependent packages - 37.5 thousand downloads total - 1 maintainer
autonomics 1.16.0
Unified Statistical Modeling of Omics Data
8 versions - Latest release: 4 months ago - 8 thousand downloads total - 3 stars on GitHub - 1 maintainer
Top 5.0% on bioconductor.org
CGHbase 1.68.0
CGHbase: Base functions and classes for arrayCGH data analysis.
5 versions - Latest release: 4 months ago - 6 dependent packages - 86.7 thousand downloads total - 0 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: about 2 months ago - 6.94 thousand downloads total - 10 stars on GitHub - 1 maintainer
a4Base 1.56.0
Automated Affymetrix Array Analysis Base Package
5 versions - Latest release: 4 months ago - 2 dependent packages - 47.6 thousand downloads total - 1 maintainer
clustifyr 1.20.0
Classifier for Single-cell RNA-seq Using Cell Clusters
7 versions - Latest release: 5 months ago - 15.4 thousand downloads total - 124 stars on GitHub - 1 maintainer
spatialHeatmap 2.14.1
spatialHeatmap: Visualizing Spatial Assays in Anatomical Images and Large-Scale Data Extensions
14 versions - Latest release: 2 months ago - 12.8 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 8.9% on bioconductor.org
MEDME 1.68.0
Modelling Experimental Data from MeDIP Enrichment
5 versions - Latest release: 4 months ago - 35 thousand downloads total - 1 maintainer
timeOmics 1.20.0
Time-Course Multi-Omics data integration
5 versions - Latest release: 5 months ago - 1 dependent package - 10.1 thousand downloads total - 21 stars on GitHub - 1 maintainer
CCPROMISE 1.34.0
PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data
5 versions - Latest release: 4 months ago - 14.4 thousand downloads total - 1 maintainer
cbaf 1.30.0
Automated functions for comparing various omic data from cbioportal.org
6 versions - Latest release: 4 months ago - 13.6 thousand downloads total - 1 maintainer
CausalR 1.40.0
Causal network analysis methods
5 versions - Latest release: 4 months ago - 18.2 thousand downloads total - 2 maintainers
diffcoexp 1.28.0
Differential Co-expression Analysis
5 versions - Latest release: 4 months ago - 16.5 thousand downloads total - 15 stars on GitHub - 1 maintainer
Top 6.5% on bioconductor.org
goProfiles 1.70.0
goProfiles: an R package for the statistical analysis of functional profiles
5 versions - Latest release: 4 months ago - 1 dependent package - 47.8 thousand downloads total - 1 maintainer
transite 1.26.0
RNA-binding protein motif analysis
6 versions - Latest release: 4 months ago - 11 thousand downloads total - 1 maintainer
Top 8.3% on bioconductor.org
MANOR 1.80.0
CGH Micro-Array NORmalization
5 versions - Latest release: 4 months ago - 37.5 thousand downloads total - 1 maintainer
Top 7.6% on bioconductor.org
Mulcom 1.58.0
Calculates Mulcom test
5 versions - Latest release: 4 months ago - 38.2 thousand downloads total - 1 maintainer
adSplit 1.78.0
Annotation-Driven Clustering
5 versions - Latest release: 4 months ago - 45.5 thousand downloads total - 1 maintainer
Top 5.4% on bioconductor.org
wateRmelon 2.14.0
Illumina DNA methylation array normalization and metrics
5 versions - Latest release: 4 months ago - 5 dependent packages - 157 thousand downloads total - 1 maintainer
trio 3.46.0
Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
5 versions - Latest release: 4 months ago - 29.8 thousand downloads total - 1 maintainer
AMOUNTAIN 1.34.0
Active modules for multilayer weighted gene co-expression networks: a continuous optimization app...
5 versions - Latest release: 4 months ago - 1 dependent package - 20.3 thousand downloads total - 1 maintainer
Top 6.3% on bioconductor.org
goTools 1.82.0
Functions for Gene Ontology database
5 versions - Latest release: 4 months ago - 49.8 thousand downloads total - 1 maintainer
shinyMethyl 1.44.0
Interactive visualization for Illumina methylation arrays
5 versions - Latest release: 4 months ago - 32.5 thousand downloads total - 6 stars on GitHub - 1 maintainer
MiChip 1.62.0
MiChip Parsing and Summarizing Functions
5 versions - Latest release: 4 months ago - 30.4 thousand downloads total - 1 maintainer
a4Classif 1.56.0
Automated Affymetrix Array Analysis Classification Package
5 versions - Latest release: 4 months ago - 1 dependent package - 44.8 thousand downloads total - 1 maintainer
ADAM 1.24.0
ADAM: Activity and Diversity Analysis Module
5 versions - Latest release: 4 months ago - 1 dependent package - 14.5 thousand downloads total - 1 maintainer
LimROTS 1.0.3
LimROTS: A Hybrid Method Integrating Empirical Bayes and Reproducibility-Optimized Statistics for...
3 versions - Latest release: about 1 month ago - 1.59 thousand downloads total - 1 stars on GitHub - 1 maintainer
SBGNview 1.22.0
"SBGNview: Data Analysis, Integration and Visualization on SBGN Pathways"
5 versions - Latest release: 4 months ago - 14.5 thousand downloads total - 28 stars on GitHub - 1 maintainer
GeoTcgaData 2.8.0
Processing Various Types of Data on GEO and TCGA
5 versions - Latest release: 4 months ago - 6.88 thousand downloads total - 28 stars on GitHub - 1 maintainer
Top 8.4% on bioconductor.org
fdrame 1.80.0
FDR adjustments of Microarray Experiments (FDR-AME)
5 versions - Latest release: 4 months ago - 37 thousand downloads total - 1 maintainer
tigre 1.62.0
Transcription factor Inference through Gaussian process Reconstruction of Expression
5 versions - Latest release: 5 months ago - 32.2 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 5.8% on bioconductor.org
fabia 2.54.0
FABIA: Factor Analysis for Bicluster Acquisition
5 versions - Latest release: 4 months ago - 3 dependent packages - 55.8 thousand downloads total - 1 maintainer
Top 9.1% on bioconductor.org
codelink 1.76.0
Manipulation of Codelink microarray data
5 versions - Latest release: 4 months ago - 1 dependent package - 40.7 thousand downloads total - 0 stars on GitHub - 2 maintainers
Top 4.5% on bioconductor.org
convert 1.84.0
Convert Microarray Data Objects
5 versions - Latest release: 4 months ago - 4 dependent packages - 76.1 thousand downloads total - 1 maintainer
geva 1.16.0
Gene Expression Variation Analysis (GEVA)
5 versions - Latest release: 4 months ago - 6.94 thousand downloads total - 2 stars on GitHub - 1 maintainer
consensusOV 1.30.0
Gene expression-based subtype classification for high-grade serous ovarian cancer
5 versions - Latest release: 4 months ago - 1 dependent package - 15.4 thousand downloads total - 1 maintainer
GEOexplorer 1.14.0
GEOexplorer: a webserver for gene expression analysis and visualisation
5 versions - Latest release: 4 months ago - 7.43 thousand downloads total - 5 stars on GitHub - 1 maintainer
miRSM 2.4.0
Inferring miRNA sponge modules in heterogeneous data
6 versions - Latest release: 4 months ago - 10.6 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 8.8% on bioconductor.org
iterativeBMA 1.66.0
The Iterative Bayesian Model Averaging (BMA) algorithm
5 versions - Latest release: 4 months ago - 34.2 thousand downloads total - 1 maintainer
Top 4.2% on bioconductor.org
GLAD 2.72.0
Gain and Loss Analysis of DNA
5 versions - Latest release: 4 months ago - 5 dependent packages - 93.4 thousand downloads total - 1 maintainer
geNetClassifier 1.48.0
Classify diseases and build associated gene networks using gene expression profiles
5 versions - Latest release: 4 months ago - 2 dependent packages - 33.8 thousand downloads total - 1 maintainer
maPredictDSC 1.46.0
Phenotype prediction using microarray data: approach of the best overall team in the IMPROVER Dia...
5 versions - Latest release: 4 months ago - 22.8 thousand downloads total - 1 maintainer
blima 1.42.0
Tools for the preprocessing and analysis of the Illumina microarrays on the detector (bead) level
5 versions - Latest release: 5 months ago - 21.1 thousand downloads total - 1 maintainer
Top 5.3% on bioconductor.org
qusage 2.42.0
qusage: Quantitative Set Analysis for Gene Expression
5 versions - Latest release: 4 months ago - 1 dependent package - 59.5 thousand downloads total - 1 maintainer
Top 4.3% on bioconductor.org
ChAMP 2.38.0
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
5 versions - Latest release: 5 months ago - 1 dependent package - 139 thousand downloads total - 1 maintainer
Top 7.6% on bioconductor.org
factDesign 1.84.0
Factorial designed microarray experiment analysis
5 versions - Latest release: 4 months ago - 40.2 thousand downloads total - 1 maintainer
normalize450K 1.36.0
Preprocessing of Illumina Infinium 450K data
5 versions - Latest release: 4 months ago - 14.1 thousand downloads total - 1 maintainer
cogena 1.42.0
co-expressed gene-set enrichment analysis
5 versions - Latest release: 4 months ago - 23.4 thousand downloads total - 12 stars on GitHub - 1 maintainer
pandaR 1.40.0
PANDA Algorithm
5 versions - Latest release: 4 months ago - 1 dependent package - 22.5 thousand downloads total - 2 maintainers
Top 5.9% on bioconductor.org
OCplus 1.82.0
Operating characteristics plus sample size and local fdr for microarray experiments
5 versions - Latest release: 5 months ago - 47.5 thousand downloads total - 1 maintainer
CNVRanger 1.24.2
Summarization and expression/phenotype association of CNV ranges
7 versions - Latest release: 3 months ago - 13.8 thousand downloads total - 4 stars on GitHub - 1 maintainer
MGFM 1.42.0
Marker Gene Finder in Microarray gene expression data
5 versions - Latest release: 4 months ago - 1 dependent package - 19.6 thousand downloads total - 1 maintainer
ROTS 2.0.0
Reproducibility-Optimized Test Statistic
5 versions - Latest release: 4 months ago - 2 dependent packages - 32.6 thousand downloads total - 1 maintainer
anota2seq 1.30.0
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
5 versions - Latest release: 4 months ago - 19 thousand downloads total - 2 maintainers
anota 1.56.0
ANalysis Of Translational Activity (ANOTA).
5 versions - Latest release: 4 months ago - 1 dependent package - 36.5 thousand downloads total - 1 maintainer
mirIntegrator 1.38.0
Integrating microRNA expression into signaling pathways for pathway analysis
5 versions - Latest release: 5 months ago - 17.1 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 7.0% on bioconductor.org
a4 1.56.0
Automated Affymetrix Array Analysis Umbrella Package
6 versions - Latest release: 4 months ago - 47.1 thousand downloads total - 1 maintainer
Top 9.9% on bioconductor.org
bgx 1.74.0
Bayesian Gene eXpression
6 versions - Latest release: 4 months ago - 42.5 thousand downloads total - 1 maintainer
MODA 1.34.0
MODA: MOdule Differential Analysis for weighted gene co-expression network
5 versions - Latest release: 4 months ago - 16 thousand downloads total - 1 maintainer
Top 4.3% on bioconductor.org
arrayQualityMetrics 3.64.0
Quality metrics report for microarray data sets
5 versions - Latest release: 5 months ago - 197 thousand downloads total - 1 stars on GitHub - 1 maintainer
DrugVsDisease 2.50.0
Comparison of disease and drug profiles using Gene set Enrichment Analysis
5 versions - Latest release: 4 months ago - 27.6 thousand downloads total - 1 maintainer
TTMap 1.30.0
Two-Tier Mapper: a clustering tool based on topological data analysis
5 versions - Latest release: 4 months ago - 11.8 thousand downloads total - 1 maintainer
Top 7.9% on bioconductor.org
SIM 1.78.0
Integrated Analysis on two human genomic datasets
5 versions - Latest release: 4 months ago - 35.3 thousand downloads total - 1 maintainer
quantiseqr 1.16.0
Quantification of the Tumor Immune contexture from RNA-seq data
5 versions - Latest release: 4 months ago - 2 dependent packages - 27.2 thousand downloads total - 1 maintainer
Top 9.3% on bioconductor.org
DFP 1.66.0
Gene Selection
5 versions - Latest release: 4 months ago - 34.2 thousand downloads total - 1 maintainer
iChip 1.62.0
Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models
5 versions - Latest release: 4 months ago - 30.2 thousand downloads total - 1 maintainer
discordant 1.32.0
The Discordant Method: A Novel Approach for Differential Correlation
5 versions - Latest release: 4 months ago - 16.9 thousand downloads total - 10 stars on GitHub - 1 maintainer
pepStat 1.42.0
Statistical analysis of peptide microarrays
5 versions - Latest release: 4 months ago - 19.2 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 9.9% on bioconductor.org
mBPCR 1.62.0
Bayesian Piecewise Constant Regression for DNA copy number estimation
5 versions - Latest release: 4 months ago - 31.7 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
maCorrPlot 1.78.0
Visualize artificial correlation in microarray data
5 versions - Latest release: 4 months ago - 33.5 thousand downloads total - 1 maintainer
Top 5.3% on bioconductor.org
puma 3.50.0
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and ex...
5 versions - Latest release: 4 months ago - 1 dependent package - 53.1 thousand downloads total - 1 maintainer
ENmix 1.44.3
Quality control and analysis tools for Illumina DNA methylation BeadChip
9 versions - Latest release: about 1 month ago - 39.3 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
illuminaio 0.50.0
Parsing Illumina Microarray Output Files
5 versions - Latest release: 4 months ago - 12 dependent packages - 482 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 4.2% on bioconductor.org
piano 2.24.0
Platform for integrative analysis of omics data
5 versions - Latest release: 4 months ago - 3 dependent packages - 81.6 thousand downloads total - 1 maintainer
Top 3.9% on bioconductor.org
made4 1.82.0
Multivariate analysis of microarray data using ADE4
5 versions - Latest release: 4 months ago - 1 dependent package - 96.5 thousand downloads total - 1 maintainer
ADaCGH2 2.48.0
Analysis of big data from aCGH experiments using parallel computing and ff objects
5 versions - Latest release: 4 months ago - 37.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
randRotation 1.20.0
Random Rotation Methods for High Dimensional Data with Batch Structure
5 versions - Latest release: 4 months ago - 7.83 thousand downloads total - 0 stars on GitHub - 1 maintainer
Related Keywords
Software 375 GeneExpression 141 DifferentialExpression 123 Preprocessing 90 RNASeq 75 Sequencing 68 Visualization 64 QualityControl 61 ImmunoOncology 60 OneChannel 58 TwoChannel 52 MultipleComparison 49 Clustering 47 GeneSetEnrichment 42 DNAMethylation 39 Transcription 38 Genetics 38 DataImport 36 Classification 35 Normalization 33 Pathways 29 GraphAndNetwork 29 CopyNumberVariation 27 Proteomics 26 Network 24 MethylationArray 23 BatchEffect 22 Transcriptomics 22 Regression 22 GO 20 SNP 19 mRNAMicroarray 19 TimeCourse 18 SystemsBiology 18 StatisticalMethod 18 DifferentialMethylation 16 Epigenetics 16 BiomedicalInformatics 16 Annotation 16 ReportWriting 14 GeneRegulation 14 Metabolomics 13 Bayesian 13 ExonArray 11 PrincipalComponent 10 GeneTarget 10 r 9 FunctionalGenomics 9 KEGG 9 Infrastructure 9 DataRepresentation 8 GeneticVariability 8 FeatureExtraction 8 ChIPSeq 8 Coverage 8 SingleCell 8 ProprietaryPlatforms 8 NetworkInference 8 bioconductor 8 AlternativeSplicing 8 DifferentialSplicing 8 GUI 7 CpGIsland 7 NetworkEnrichment 7 bioconductor-package 6 GenomeAnnotation 6 bioinformatics 6 MicroRNAArray 6 DimensionReduction 6 MultiChannel 5 CellBiology 5 GenePrediction 5 MethylSeq 5 GenomeWideAssociation 5 Spatial 4 TissueMicroarray 4 aCGH 4 GenomicVariation 4 ChIPchip 4 genomics 4 WholeGenome 4 package 4 Metagenomics 3 ResearchField 3 DNASeq 3 GeneSignaling 3 Alignment 3 Technology 3 SequenceMatching 3 transcriptomics 3 Survival 3 Reactome 3 MassSpectrometry 3 differential-expression 2 Cancer 2 AnnotationData 2 enrichment-analysis 2 DecisionTree 2 FlowCytometry 2 AgilentChip 2