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An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.

bioconductor.org "Microarray" keyword

Top 2.6% on bioconductor.org
mixOmics 6.34.0
Omics Data Integration Project
6 versions - Latest release: 5 months ago - 9 dependent packages - 372 thousand downloads total - 1 maintainer
PROMISE 1.62.0
PRojection Onto the Most Interesting Statistical Evidence
6 versions - Latest release: 5 months ago - 1 dependent package - 33.9 thousand downloads total - 2 maintainers
Top 1.7% on bioconductor.org
sva 3.58.0
Surrogate Variable Analysis
7 versions - Latest release: 6 months ago - 43 dependent packages - 1.2 million downloads total - 3 maintainers
Top 9.9% on bioconductor.org
tilingArray 1.88.0
Transcript mapping with high-density oligonucleotide tiling arrays
6 versions - Latest release: 5 months ago - 2 dependent packages - 62.5 thousand downloads total - 1 maintainer
mirIntegrator 1.40.0
Integrating microRNA expression into signaling pathways for pathway analysis
6 versions - Latest release: 5 months ago - 20.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 0.9% on bioconductor.org
affy 1.88.0
Methods for Affymetrix Oligonucleotide Arrays
6 versions - Latest release: 6 months ago - 74 dependent packages - 2.27 million downloads total - 1 maintainer
Top 5.8% on bioconductor.org
CNTools 1.66.0
Convert segment data into a region by sample matrix to allow for other high level computational a...
6 versions - Latest release: 5 months ago - 1 dependent package - 67.2 thousand downloads total - 1 maintainer
Top 1.8% on bioconductor.org
lumi 2.62.0
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
6 versions - Latest release: 6 months ago - 10 dependent packages - 410 thousand downloads total - 1 maintainer
Top 6.2% on bioconductor.org
arrayQuality 1.88.0
Assessing array quality on spotted arrays
6 versions - Latest release: 5 months ago - 77.1 thousand downloads total - 1 maintainer
Top 0.7% on bioconductor.org
genefilter 1.92.0
genefilter: methods for filtering genes from high-throughput experiments
6 versions - Latest release: 5 months ago - 66 dependent packages - 4.2 million downloads total - 1 maintainer
Top 2.3% on bioconductor.org
ReportingTools 2.50.0
Tools for making reports in various formats
7 versions - Latest release: 5 months ago - 5 dependent packages - 246 thousand downloads total - 3 maintainers
Top 1.2% on bioconductor.org
multtest 2.66.0
Resampling-based multiple hypothesis testing
6 versions - Latest release: 5 months ago - 37 dependent packages - 2.67 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
vsn 3.78.1
Variance stabilization and calibration for microarray data
7 versions - Latest release: 3 months ago - 30 dependent packages - 1.19 million downloads total - 1 maintainer
Top 9.0% on bioconductor.org
RLMM 1.72.0
A Genotype Calling Algorithm for Affymetrix SNP Arrays
6 versions - Latest release: 5 months ago - 35.8 thousand downloads total - 1 maintainer
Top 1.9% on bioconductor.org
minfi 1.56.0
Analyze Illumina Infinium DNA methylation arrays
8 versions - Latest release: 5 months ago - 31 dependent packages - 954 thousand downloads total - 63 stars on GitHub - 1 maintainer
Top 1.3% on bioconductor.org
impute 1.84.0
impute: Imputation for microarray data
6 versions - Latest release: 6 months ago - 44 dependent packages - 2 million downloads total - 1 maintainer
IdeoViz 1.46.0
Plots data (continuous/discrete) along chromosomal ideogram
6 versions - Latest release: 5 months ago - 29.5 thousand downloads total - 1 maintainer
Top 1.4% on bioconductor.org
GEOquery 2.78.0
Get data from NCBI Gene Expression Omnibus (GEO)
6 versions - Latest release: 6 months ago - 47 dependent packages - 2.38 million downloads total - 110 stars on GitHub - 1 maintainer
Cormotif 1.56.0
Correlation Motif Fit
6 versions - Latest release: 5 months ago - 32.2 thousand downloads total - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.66.0
Linear Models for Microarray and Omics Data
16 versions - Latest release: 5 months ago - 322 dependent packages - 7.07 million downloads total - 1 maintainer
Top 6.3% on bioconductor.org
gpls 1.82.0
Classification using generalized partial least squares
6 versions - Latest release: 5 months ago - 1 dependent package - 69.6 thousand downloads total - 1 maintainer
scPCA 1.24.0
Sparse Contrastive Principal Component Analysis
6 versions - Latest release: 5 months ago - 15.3 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 7.3% on bioconductor.org
annotationTools 1.84.0
Annotate microarrays and perform cross-species gene expression analyses using flat file databases
6 versions - Latest release: 5 months ago - 1 dependent package - 60.3 thousand downloads total - 1 maintainer
sampleClassifier 1.34.0
Sample Classifier
7 versions - Latest release: 2 months ago - 16 thousand downloads total - 1 maintainer
MCbiclust 1.34.0
Massive correlating biclusters for gene expression data and associated methods
6 versions - Latest release: 5 months ago - 19.4 thousand downloads total - 1 maintainer
Top 9.9% on bioconductor.org
affyio 1.80.0
Tools for parsing Affymetrix data files
6 versions - Latest release: 5 months ago - 12 dependent packages - 1.94 million downloads total - 3 stars on GitHub - 1 maintainer
rain 1.44.0
Rhythmicity Analysis Incorporating Non-parametric Methods
6 versions - Latest release: 5 months ago - 29.2 thousand downloads total - 1 maintainer
randRotation 1.22.0
Random Rotation Methods for High Dimensional Data with Batch Structure
6 versions - Latest release: 5 months ago - 9.97 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 2.8% on bioconductor.org
DECIPHER 3.6.0
Tools for curating, analyzing, and manipulating biological sequences
6 versions - Latest release: 5 months ago - 7 dependent packages - 365 thousand downloads total - 1 maintainer
roastgsa 1.8.0
Rotation based gene set analysis
5 versions - Latest release: 5 months ago - 6.34 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 9.1% on bioconductor.org
pickgene 1.82.0
Adaptive Gene Picking for Microarray Expression Data Analysis
6 versions - Latest release: 5 months ago - 35.4 thousand downloads total - 1 maintainer
twilight 1.86.0
Estimation of local false discovery rate
6 versions - Latest release: 5 months ago - 1 dependent package - 56.7 thousand downloads total - 1 maintainer
PECA 1.46.0
Probe-level Expression Change Averaging
6 versions - Latest release: 5 months ago - 1 dependent package - 27.2 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
globaltest 5.64.0
Testing Groups of Covariates/Features for Association with a Response Variable, with Applications...
6 versions - Latest release: 5 months ago - 6 dependent packages - 308 thousand downloads total - 1 maintainer
AMOUNTAIN 1.36.0
Active modules for multilayer weighted gene co-expression networks: a continuous optimization app...
6 versions - Latest release: 5 months ago - 1 dependent package - 23.3 thousand downloads total - 1 maintainer
netresponse 1.70.0
Functional Network Analysis
6 versions - Latest release: 5 months ago - 34.4 thousand downloads total - 3 stars on GitHub - 1 maintainer
affyPLM 1.86.0
Methods for fitting probe-level models
6 versions - Latest release: 5 months ago - 9 dependent packages - 638 thousand downloads total - 0 stars on GitHub - 1 maintainer
TOAST 1.24.0
Tools for the analysis of heterogeneous tissues
6 versions - Latest release: 5 months ago - 3 dependent packages - 38.1 thousand downloads total - 8 stars on GitHub - 1 maintainer
MODA 1.36.0
MODA: MOdule Differential Analysis for weighted gene co-expression network
6 versions - Latest release: 5 months ago - 18.8 thousand downloads total - 1 maintainer
Top 2.2% on bioconductor.org
marray 1.88.0
Exploratory analysis for two-color spotted microarray data
6 versions - Latest release: 5 months ago - 21 dependent packages - 658 thousand downloads total - 1 maintainer
Top 3.8% on bioconductor.org
aroma.light 3.40.0
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Da...
6 versions - Latest release: 5 months ago - 3 dependent packages - 423 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 6.3% on bioconductor.org
goTools 1.84.0
Functions for Gene Ontology database
6 versions - Latest release: 5 months ago - 53.8 thousand downloads total - 1 maintainer
Top 7.9% on bioconductor.org
mdqc 1.72.0
Mahalanobis Distance Quality Control for microarrays
6 versions - Latest release: 5 months ago - 1 dependent package - 44.6 thousand downloads total - 1 maintainer
Top 8.4% on bioconductor.org
TEQC 4.32.0
Quality control for target capture experiments
6 versions - Latest release: 5 months ago - 38 thousand downloads total - 1 maintainer
Top 9.1% on bioconductor.org
Harshlight 1.82.0
A "corrective make-up" program for microarray chips
6 versions - Latest release: 5 months ago - 39.8 thousand downloads total - 1 maintainer
Top 9.5% on bioconductor.org
multiscan 1.70.0
R package for combining multiple scans
6 versions - Latest release: 5 months ago - 35.4 thousand downloads total - 1 maintainer
CAFE 1.46.0
Chromosmal Aberrations Finder in Expression data
6 versions - Latest release: 5 months ago - 27.4 thousand downloads total - 1 maintainer
Top 2.3% on bioconductor.org
GOstats 2.76.0
Tools for manipulating GO and microarrays
6 versions - Latest release: 5 months ago - 23 dependent packages - 594 thousand downloads total - 1 maintainer
GSRI 2.58.0
Gene Set Regulation Index
6 versions - Latest release: 5 months ago - 35 thousand downloads total - 1 maintainer
biotmle 1.34.0
Targeted Learning with Moderated Statistics for Biomarker Discovery
7 versions - Latest release: 5 months ago - 20.4 thousand downloads total - 1 maintainer
Top 5.8% on bioconductor.org
fabia 2.56.0
FABIA: Factor Analysis for Bicluster Acquisition
6 versions - Latest release: 5 months ago - 3 dependent packages - 60.7 thousand downloads total - 1 maintainer
ADAM 1.26.0
ADAM: Activity and Diversity Analysis Module
6 versions - Latest release: 5 months ago - 1 dependent package - 17.5 thousand downloads total - 1 maintainer
Top 3.4% on bioconductor.org
rGADEM 2.58.0
de novo motif discovery
7 versions - Latest release: 2 months ago - 1 dependent package - 109 thousand downloads total - 1 maintainer
Top 5.6% on bioconductor.org
RDRToolbox 1.60.0
A package for nonlinear dimension reduction with Isomap and LLE.
6 versions - Latest release: 5 months ago - 53.4 thousand downloads total - 1 maintainer
Top 7.0% on bioconductor.org
a4 1.58.0
Automated Affymetrix Array Analysis Umbrella Package
7 versions - Latest release: 5 months ago - 51.1 thousand downloads total - 1 maintainer
cn.farms 1.58.0
cn.FARMS - factor analysis for copy number estimation
7 versions - Latest release: 5 months ago - 46.2 thousand downloads total - 1 maintainer
zenith 1.12.0
Gene set analysis following differential expression using linear (mixed) modeling with dream
7 versions - Latest release: 5 months ago - 2 dependent packages - 13 thousand downloads total - 0 stars on GitHub - 1 maintainer
ExiMiR 2.52.0
R functions for the normalization of Exiqon miRNA array data
6 versions - Latest release: 5 months ago - 34.6 thousand downloads total - 1 maintainer
ccmap 1.36.0
Combination Connectivity Mapping
6 versions - Latest release: 5 months ago - 19.6 thousand downloads total - 1 maintainer
Top 3.1% on bioconductor.org
RankProd 3.36.0
Rank Product method for identifying differentially expressed genes with application in meta-analysis
6 versions - Latest release: 5 months ago - 4 dependent packages - 128 thousand downloads total - 1 maintainer
phantasus 1.30.0
Visual and interactive gene expression analysis
6 versions - Latest release: 5 months ago - 21.2 thousand downloads total - 1 maintainer
Top 9.3% on bioconductor.org
DFP 1.68.0
Gene Selection
6 versions - Latest release: 5 months ago - 37.9 thousand downloads total - 1 maintainer
CellScore 1.30.0
Tool for Evaluation of Cell Identity from Transcription Profiles
6 versions - Latest release: 5 months ago - 12.8 thousand downloads total - 1 maintainer
Top 5.3% on bioconductor.org
qusage 2.44.0
qusage: Quantitative Set Analysis for Gene Expression
6 versions - Latest release: 5 months ago - 1 dependent package - 69.7 thousand downloads total - 1 maintainer
maPredictDSC 1.48.0
Phenotype prediction using microarray data: approach of the best overall team in the IMPROVER Dia...
6 versions - Latest release: 5 months ago - 25.9 thousand downloads total - 1 maintainer
Top 4.3% on bioconductor.org
arrayQualityMetrics 3.66.0
Quality metrics report for microarray data sets
7 versions - Latest release: 2 months ago - 217 thousand downloads total - 1 stars on GitHub - 1 maintainer
annmap 1.52.0
Genome annotation and visualisation package pertaining to Affymetrix arrays and NGS analysis.
6 versions - Latest release: 5 months ago - 29.3 thousand downloads total - 0 stars on GitHub - 1 maintainer
MiChip 1.64.0
MiChip Parsing and Summarizing Functions
6 versions - Latest release: 5 months ago - 33.9 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
minet 3.68.0
Mutual Information NETworks
6 versions - Latest release: 5 months ago - 9 dependent packages - 169 thousand downloads total - 1 maintainer
Top 4.5% on bioconductor.org
ArrayExpress 1.70.0
Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures:...
7 versions - Latest release: 5 months ago - 1 dependent package - 154 thousand downloads total - 1 maintainer
anota 1.58.0
ANalysis Of Translational Activity (ANOTA).
6 versions - Latest release: 5 months ago - 1 dependent package - 40.1 thousand downloads total - 1 maintainer
Pigengene 1.36.0
Infers biological signatures from gene expression data
7 versions - Latest release: 6 days ago - 1 dependent package - 22.2 thousand downloads total - 1 maintainer
quantiseqr 1.18.0
Quantification of the Tumor Immune contexture from RNA-seq data
6 versions - Latest release: 5 months ago - 2 dependent packages - 38.1 thousand downloads total - 1 maintainer
Top 4.2% on bioconductor.org
piano 2.26.0
Platform for integrative analysis of omics data
6 versions - Latest release: 5 months ago - 3 dependent packages - 107 thousand downloads total - 1 maintainer
a4Classif 1.58.0
Automated Affymetrix Array Analysis Classification Package
6 versions - Latest release: 5 months ago - 1 dependent package - 48.8 thousand downloads total - 1 maintainer
Top 8.8% on bioconductor.org
nnNorm 2.74.0
Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
6 versions - Latest release: 5 months ago - 38.2 thousand downloads total - 1 maintainer
Top 7.0% on bioconductor.org
SpeCond 1.64.0
Condition specific detection from expression data
6 versions - Latest release: 5 months ago - 41.9 thousand downloads total - 1 maintainer
Top 9.9% on bioconductor.org
mBPCR 1.64.0
Bayesian Piecewise Constant Regression for DNA copy number estimation
6 versions - Latest release: 5 months ago - 35.6 thousand downloads total - 1 maintainer
consensus 1.28.0
Cross-platform consensus analysis of genomic measurements via interlaboratory testing method
6 versions - Latest release: 5 months ago - 13 thousand downloads total - 1 maintainer
Top 6.5% on bioconductor.org
GeneMeta 1.82.0
MetaAnalysis for High Throughput Experiments
6 versions - Latest release: 5 months ago - 2 dependent packages - 53.1 thousand downloads total - 1 maintainer
RRHO 1.50.0
Inference on agreement between ordered lists
6 versions - Latest release: 5 months ago - 29.8 thousand downloads total - 1 maintainer
AGDEX 1.58.0
Agreement of Differential Expression Analysis
6 versions - Latest release: 5 months ago - 38.2 thousand downloads total - 1 maintainer
Harman 1.38.0
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
6 versions - Latest release: 5 months ago - 1 dependent package - 31.8 thousand downloads total - 1 maintainer
HDTD 1.44.0
Statistical Inference about the Mean Matrix and the Covariance Matrices in High-Dimensional Trans...
6 versions - Latest release: 5 months ago - 20.8 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 3.9% on bioconductor.org
pathview 1.50.0
a tool set for pathway based data integration and visualization
6 versions - Latest release: 5 months ago - 9 dependent packages - 706 thousand downloads total - 41 stars on GitHub - 1 maintainer
mCSEA 1.30.1
Methylated CpGs Set Enrichment Analysis
8 versions - Latest release: 4 months ago - 1 dependent package - 18.5 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
a4Preproc 1.58.0
Automated Affymetrix Array Analysis Preprocessing Package
6 versions - Latest release: 5 months ago - 4 dependent packages - 57.8 thousand downloads total - 1 maintainer
ROTS 2.2.0
Reproducibility-Optimized Test Statistic
6 versions - Latest release: 5 months ago - 2 dependent packages - 41.4 thousand downloads total - 1 maintainer
Top 7.6% on bioconductor.org
factDesign 1.86.0
Factorial designed microarray experiment analysis
6 versions - Latest release: 5 months ago - 44.3 thousand downloads total - 1 maintainer
EMDomics 2.40.0
Earth Mover's Distance for Differential Analysis of Genomics Data
6 versions - Latest release: 5 months ago - 23.5 thousand downloads total - 1 maintainer
MGFM 1.44.0
Marker Gene Finder in Microarray gene expression data
6 versions - Latest release: 5 months ago - 1 dependent package - 22.8 thousand downloads total - 1 maintainer
Top 2.7% on bioconductor.org
Gviz 1.54.0
Plotting data and annotation information along genomic coordinates
7 versions - Latest release: 5 months ago - 57 dependent packages - 1.04 million downloads total - 87 stars on GitHub - 1 maintainer
Top 7.8% on bioconductor.org
AgiMicroRna 2.60.0
Processing and Differential Expression Analysis of Agilent microRNA chips
6 versions - Latest release: 5 months ago - 60.9 thousand downloads total - 1 maintainer
Top 8.4% on bioconductor.org
fdrame 1.82.0
FDR adjustments of Microarray Experiments (FDR-AME)
6 versions - Latest release: 5 months ago - 40.4 thousand downloads total - 1 maintainer
Rnits 1.44.0
R Normalization and Inference of Time Series data
6 versions - Latest release: 5 months ago - 22 thousand downloads total - 1 maintainer
Top 6.2% on bioconductor.org
cghMCR 1.68.0
Find chromosome regions showing common gains/losses
6 versions - Latest release: 5 months ago - 61.4 thousand downloads total - 1 maintainer
MEAL 1.40.0
Perform methylation analysis
6 versions - Latest release: 5 months ago - 24.3 thousand downloads total - 1 maintainer
consensusOV 1.32.0
Gene expression-based subtype classification for high-grade serous ovarian cancer
6 versions - Latest release: 5 months ago - 1 dependent package - 18.7 thousand downloads total - 1 maintainer
xCell2 1.2.3
A Tool for Generic Cell Type Enrichment Analysis
7 versions - Latest release: 4 months ago - 5.29 thousand downloads total - 11 stars on GitHub - 1 maintainer
geNetClassifier 1.50.0
Classify diseases and build associated gene networks using gene expression profiles
6 versions - Latest release: 5 months ago - 2 dependent packages - 37.6 thousand downloads total - 1 maintainer
Related Keywords
Software 375 GeneExpression 142 DifferentialExpression 123 Preprocessing 90 RNASeq 75 Sequencing 69 Visualization 64 QualityControl 61 ImmunoOncology 60 OneChannel 58 TwoChannel 52 MultipleComparison 49 Clustering 47 GeneSetEnrichment 43 DNAMethylation 39 Transcription 38 Genetics 38 DataImport 36 Classification 35 Normalization 33 Pathways 30 GraphAndNetwork 29 CopyNumberVariation 27 Proteomics 26 Network 24 Transcriptomics 23 MethylationArray 23 BatchEffect 22 Regression 22 GO 21 mRNAMicroarray 19 SNP 19 SystemsBiology 19 StatisticalMethod 18 TimeCourse 18 Annotation 17 Epigenetics 16 DifferentialMethylation 16 BiomedicalInformatics 16 ReportWriting 14 GeneRegulation 14 Metabolomics 13 Bayesian 13 ExonArray 11 GeneTarget 10 PrincipalComponent 10 Infrastructure 9 r 9 KEGG 9 FunctionalGenomics 9 DataRepresentation 8 GeneticVariability 8 NetworkInference 8 ProprietaryPlatforms 8 bioconductor 8 DifferentialSplicing 8 SingleCell 8 Coverage 8 ChIPSeq 8 AlternativeSplicing 8 FeatureExtraction 8 GUI 7 CpGIsland 7 NetworkEnrichment 7 DimensionReduction 6 MicroRNAArray 6 bioinformatics 6 GenomeAnnotation 6 bioconductor-package 6 GenePrediction 5 MethylSeq 5 MultiChannel 5 GenomeWideAssociation 5 CellBiology 5 aCGH 4 ChIPchip 4 TissueMicroarray 4 Spatial 4 GenomicVariation 4 package 4 genomics 4 WholeGenome 4 Metagenomics 3 Technology 3 transcriptomics 3 DNASeq 3 MassSpectrometry 3 Reactome 3 Alignment 3 SequenceMatching 3 ResearchField 3 GeneSignaling 3 Survival 3 Bioinformatics 2 differential-expression 2 cerna 2 mirna 2 AssayDomain 2 Cancer 2 SAGE 2