Ecosyste.ms: Packages

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

bioconductor.org "Microarray" keyword

gemma.R 3.0.3
A wrapper for Gemma's Restful API to access curated gene expression data and differential express...
6 versions - Latest release: 6 days ago - 2.01 thousand downloads total - 9 stars on GitHub - 1 maintainer
DrugVsDisease 2.44.0
Comparison of disease and drug profiles using Gene set Enrichment Analysis
3 versions - Latest release: 6 months ago - 22.1 thousand downloads total - 1 maintainer
Top 8.2% on bioconductor.org
macat 1.76.0 removed
MicroArray Chromosome Analysis Tool
2 versions - Latest release: 6 months ago - 29.9 thousand downloads total - 1 maintainer
Top 6.2% on bioconductor.org
cghMCR 1.60.0
Find chromosome regions showing common gains/losses
3 versions - Latest release: 6 months ago - 50.4 thousand downloads total - 1 maintainer
quantiseqr 1.10.0
Quantification of the Tumor Immune contexture from RNA-seq data
3 versions - Latest release: 6 months ago - 2 dependent packages - 11.8 thousand downloads total - 1 maintainer
SNAGEE 1.42.0
Signal-to-Noise applied to Gene Expression Experiments
3 versions - Latest release: 6 months ago - 18.3 thousand downloads total - 1 maintainer
npGSEA 1.38.0
Permutation approximation methods for gene set enrichment analysis (non-permutation GSEA)
3 versions - Latest release: 6 months ago - 17.7 thousand downloads total - 1 maintainer
Top 7.6% on bioconductor.org
factDesign 1.78.0
Factorial designed microarray experiment analysis
3 versions - Latest release: 6 months ago - 34.6 thousand downloads total - 1 maintainer
Top 7.5% on bioconductor.org
BHC 1.54.0
Bayesian Hierarchical Clustering
3 versions - Latest release: 6 months ago - 41.6 thousand downloads total - 1 maintainer
MODA 1.28.0
MODA: MOdule Differential Analysis for weighted gene co-expression network
3 versions - Latest release: 6 months ago - 11.5 thousand downloads total - 1 maintainer
TransView 1.46.0
Read density map construction and accession. Visualization of ChIPSeq and RNASeq data sets
3 versions - Latest release: 6 months ago - 21.6 thousand downloads total - 1 maintainer
mAPKL 1.32.0 removed
A Hybrid Feature Selection method for gene expression data
2 versions - Latest release: 6 months ago - 11.8 thousand downloads total - 1 maintainer
autonomics 1.12.0
Unified statistal Modeling of Omics Data
4 versions - Latest release: 15 days ago - 3.18 thousand downloads total - 3 stars on GitHub - 1 maintainer
shinyepico 1.10.0
ShinyÉPICo
3 versions - Latest release: 6 months ago - 3.54 thousand downloads total - 3 stars on GitHub - 1 maintainer
MethylAid 1.36.0
Visual and interactive quality control of large Illumina DNA Methylation array data sets
3 versions - Latest release: 6 months ago - 18.5 thousand downloads total - 1 maintainer
anota2seq 1.24.0
Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq
3 versions - Latest release: 6 months ago - 11.1 thousand downloads total - 2 maintainers
Top 8.1% on bioconductor.org
maigesPack 1.66.0
Functions to handle cDNA microarray data, including several methods of data analysis
3 versions - Latest release: 6 months ago - 30.1 thousand downloads total - 1 maintainer
Top 8.9% on bioconductor.org
altcdfenvs 2.64.0
alternative CDF environments (aka probeset mappings)
3 versions - Latest release: 6 months ago - 1 dependent package - 39.6 thousand downloads total - 1 maintainer
doppelgangR 1.30.0
Identify likely duplicate samples from genomic or meta-data
3 versions - Latest release: 6 months ago - 12.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 8.0% on bioconductor.org
OLIN 1.80.0
Optimized local intensity-dependent normalisation of two-color microarrays
3 versions - Latest release: 6 months ago - 2 dependent packages - 31 thousand downloads total - 1 maintainer
Top 9.4% on bioconductor.org
HEM 1.74.0
Heterogeneous error model for identification of differentially expressed genes under multiple con...
3 versions - Latest release: 6 months ago - 29.5 thousand downloads total - 1 maintainer
Top 7.3% on bioconductor.org
plgem 1.74.0
Detect differential expression in microarray and proteomics datasets with the Power Law Global Er...
3 versions - Latest release: 6 months ago - 1 dependent package - 34.1 thousand downloads total - 1 maintainer
phantasus 1.22.2
Visual and interactive gene expression analysis
3 versions - Latest release: 6 months ago - 11 thousand downloads total - 1 maintainer
tigre 1.56.0
Transcription factor Inference through Gaussian process Reconstruction of Expression
3 versions - Latest release: 6 months ago - 26.5 thousand downloads total - 1 stars on GitHub - 1 maintainer
TOAST 1.16.0
Tools for the analysis of heterogeneous tissues
3 versions - Latest release: 6 months ago - 3 dependent packages - 15.7 thousand downloads total - 8 stars on GitHub - 1 maintainer
anota 1.50.0
ANalysis Of Translational Activity (ANOTA).
3 versions - Latest release: 6 months ago - 1 dependent package - 29.3 thousand downloads total - 1 maintainer
dcGSA 1.30.0
Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles
3 versions - Latest release: 6 months ago - 10.5 thousand downloads total - 1 maintainer
Top 6.5% on bioconductor.org
GeneMeta 1.74.0
MetaAnalysis for High Throughput Experiments
3 versions - Latest release: 6 months ago - 2 dependent packages - 39.6 thousand downloads total - 1 maintainer
ADaCGH2 2.42.0
Analysis of big data from aCGH experiments using parallel computing and ff objects
3 versions - Latest release: 6 months ago - 30.1 thousand downloads total - 0 stars on GitHub - 1 maintainer
BatchQC 1.30.0
Batch Effects Quality Control Software
3 versions - Latest release: 6 months ago - 20.5 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 6.0% on bioconductor.org
BioNet 1.62.0
Routines for the functional analysis of biological networks
3 versions - Latest release: 6 months ago - 3 dependent packages - 63.4 thousand downloads total - 1 maintainer
COHCAP 1.48.0
CpG Island Analysis Pipeline for Illumina Methylation Array and Targeted BS-Seq Data
3 versions - Latest release: 6 months ago - 19.8 thousand downloads total - 1 maintainer
CGHnormaliter 1.56.0
Normalization of array CGH data with imbalanced aberrations.
3 versions - Latest release: 6 months ago - 28.1 thousand downloads total - 1 maintainer
Top 7.6% on bioconductor.org
Mulcom 1.52.0
Calculates Mulcom test
3 versions - Latest release: 6 months ago - 32.6 thousand downloads total - 1 maintainer
crossmeta 1.28.0
Cross Platform Meta-Analysis of Microarray Data
3 versions - Latest release: 6 months ago - 1 dependent package - 15.8 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 7.9% on bioconductor.org
RPA 1.58.0
RPA: Robust Probabilistic Averaging for probe-level analysis
3 versions - Latest release: 6 months ago - 1 dependent package - 30.5 thousand downloads total - 1 maintainer
DMRforPairs 1.38.0 removed
DMRforPairs: identifying Differentially Methylated Regions between unique samples using array bas...
2 versions - Latest release: 6 months ago - 16 thousand downloads total - 1 maintainer
geva 1.10.0
Gene Expression Variation Analysis (GEVA)
3 versions - Latest release: 6 months ago - 2.79 thousand downloads total - 2 stars on GitHub - 1 maintainer
consensusOV 1.24.0
Gene expression-based subtype classification for high-grade serous ovarian cancer
3 versions - Latest release: 6 months ago - 1 dependent package - 9.83 thousand downloads total - 1 maintainer
DeMixT 1.18.0
Cell type-specific deconvolution of heterogeneous tumor samples with two or three components usin...
3 versions - Latest release: 6 months ago - 7.82 thousand downloads total - 1 maintainer
flowVS 1.34.0
Variance stabilization in flow cytometry (and microarrays)
3 versions - Latest release: 6 months ago - 16 thousand downloads total - 1 maintainer
CeTF 1.14.0
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation an...
3 versions - Latest release: 6 months ago - 6.04 thousand downloads total - 1 maintainer
ffpe 1.46.0
Quality assessment and control for FFPE microarray expression data
3 versions - Latest release: 6 months ago - 25.1 thousand downloads total - 1 maintainer
Top 9.1% on bioconductor.org
pickgene 1.74.0
Adaptive Gene Picking for Microarray Expression Data Analysis
3 versions - Latest release: 6 months ago - 27.4 thousand downloads total - 1 maintainer
Top 9.2% on bioconductor.org
Rmagpie 1.58.0
MicroArray Gene-expression-based Program In Error rate estimation
3 versions - Latest release: 6 months ago - 27 thousand downloads total - 1 maintainer
TTMap 1.24.0
Two-Tier Mapper: a clustering tool based on topological data analysis
3 versions - Latest release: 6 months ago - 6.96 thousand downloads total - 1 maintainer
Top 7.0% on bioconductor.org
SCAN.UPC 2.44.0
Single-channel array normalization (SCAN) and Universal exPression Codes (UPC)
3 versions - Latest release: 6 months ago - 35.2 thousand downloads total - 1 maintainer
Top 7.9% on bioconductor.org
quantro 1.36.0
A test for when to use quantile normalization
3 versions - Latest release: 6 months ago - 3 dependent packages - 32.9 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
metahdep 1.60.0
Hierarchical Dependence in Meta-Analysis
3 versions - Latest release: 6 months ago - 26.7 thousand downloads total - 1 maintainer
conumee 1.36.0
Enhanced copy-number variation analysis using Illumina DNA methylation arrays
3 versions - Latest release: 6 months ago - 23.8 thousand downloads total - 1 maintainer
Top 7.4% on bioconductor.org
RefPlus 1.72.0
A function set for the Extrapolation Strategy (RMA+) and Extrapolation Averaging (RMA++) methods.
3 versions - Latest release: 6 months ago - 31.9 thousand downloads total - 1 maintainer
Top 9.1% on bioconductor.org
KCsmart 2.60.0
Multi sample aCGH analysis package using kernel convolution
3 versions - Latest release: 6 months ago - 28.4 thousand downloads total - 1 maintainer
CellMapper 1.28.0
Predict genes expressed selectively in specific cell types
3 versions - Latest release: 6 months ago - 10.5 thousand downloads total - 1 maintainer
pwrEWAS 1.16.0 removed
A user-friendly tool for comprehensive power estimation for epigenome wide association studies (E...
2 versions - Latest release: 6 months ago - 4.88 thousand downloads total - 1 maintainer
NetActivity 1.4.0
Compute gene set scores from a deep learning framework
3 versions - Latest release: 6 months ago - 1.6 thousand downloads total - 1 maintainer
Top 8.7% on bioconductor.org
genArise 1.78.0
Microarray Analysis tool
3 versions - Latest release: 6 months ago - 29.8 thousand downloads total - 1 maintainer
Top 6.7% on bioconductor.org
LPE 1.76.0
Methods for analyzing microarray data using Local Pooled Error (LPE) method
3 versions - Latest release: 6 months ago - 3 dependent packages - 38.1 thousand downloads total - 1 maintainer
Top 8.8% on bioconductor.org
iterativeBMA 1.60.0
The Iterative Bayesian Model Averaging (BMA) algorithm
3 versions - Latest release: 6 months ago - 28.9 thousand downloads total - 1 maintainer
bigmelon 1.28.0
Illumina methylation array analysis for large experiments
3 versions - Latest release: 6 months ago - 12.3 thousand downloads total - 1 maintainer
geNetClassifier 1.42.0
Classify diseases and build associated gene networks using gene expression profiles
3 versions - Latest release: 6 months ago - 2 dependent packages - 26.2 thousand downloads total - 1 maintainer
Top 8.2% on bioconductor.org
XDE 2.48.0
XDE: a Bayesian hierarchical model for cross-study analysis of differential gene expression
3 versions - Latest release: 6 months ago - 28.8 thousand downloads total - 1 maintainer
lmdme 1.44.0
Linear Model decomposition for Designed Multivariate Experiments
3 versions - Latest release: 6 months ago - 21.4 thousand downloads total - 1 maintainer
qsmooth 1.18.0
Smooth quantile normalization
3 versions - Latest release: 6 months ago - 7.31 thousand downloads total - 1 maintainer
a4Classif 1.50.0
Automated Affymetrix Array Analysis Classification Package
3 versions - Latest release: 6 months ago - 1 dependent package - 37.5 thousand downloads total - 1 maintainer
ROTS 1.30.0
Reproducibility-Optimized Test Statistic
3 versions - Latest release: 6 months ago - 2 dependent packages - 23.4 thousand downloads total - 1 maintainer
Top 9.6% on bioconductor.org
LPEadj 1.62.0 removed
A correction of the local pooled error (LPE) method to replace the asymptotic variance adjustment...
2 versions - Latest release: 6 months ago - 26.7 thousand downloads total - 1 maintainer
CoGAPS 3.22.0
Coordinated Gene Activity in Pattern Sets
3 versions - Latest release: 6 months ago - 3 dependent packages - 29.2 thousand downloads total - 4 maintainers
coGPS 1.46.0
cancer outlier Gene Profile Sets
3 versions - Latest release: 6 months ago - 21.9 thousand downloads total - 1 maintainer
CAFE 1.38.0
Chromosmal Aberrations Finder in Expression data
3 versions - Latest release: 6 months ago - 17.6 thousand downloads total - 1 maintainer
GSRI 2.50.0
Gene Set Regulation Index
3 versions - Latest release: 6 months ago - 25.8 thousand downloads total - 1 maintainer
iBMQ 1.42.0
integrated Bayesian Modeling of eQTL data
3 versions - Latest release: 6 months ago - 16.8 thousand downloads total - 1 maintainer
PECA 1.38.0
Probe-level Expression Change Averaging
3 versions - Latest release: 6 months ago - 1 dependent package - 17.8 thousand downloads total - 1 maintainer
Top 6.5% on bioconductor.org
interactiveDisplay 1.40.0
Package for enabling powerful shiny web displays of Bioconductor objects
3 versions - Latest release: 6 months ago - 1 dependent package - 39.9 thousand downloads total - 1 maintainer
Top 6.6% on bioconductor.org
GSEAlm 1.62.0
Linear Model Toolset for Gene Set Enrichment Analysis
3 versions - Latest release: 6 months ago - 41.4 thousand downloads total - 1 maintainer
Top 8.1% on bioconductor.org
MiPP 1.74.0
Misclassification Penalized Posterior Classification
3 versions - Latest release: 6 months ago - 30.8 thousand downloads total - 1 maintainer
snm 1.50.0
Supervised Normalization of Microarrays
3 versions - Latest release: 6 months ago - 1 dependent package - 35.5 thousand downloads total - 1 maintainer
Top 9.3% on bioconductor.org
DFP 1.60.0
Gene Selection
3 versions - Latest release: 6 months ago - 28.8 thousand downloads total - 1 maintainer
iChip 1.56.0
Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models
3 versions - Latest release: 6 months ago - 24.4 thousand downloads total - 1 maintainer
Top 8.8% on bioconductor.org
nnNorm 2.66.0
Spatial and intensity based normalization of cDNA microarray data based on robust neural nets
3 versions - Latest release: 6 months ago - 28.7 thousand downloads total - 1 maintainer
a4Reporting 1.50.0
Automated Affymetrix Array Analysis Reporting Package
3 versions - Latest release: 6 months ago - 1 dependent package - 34.3 thousand downloads total - 1 maintainer
pepStat 1.36.0
Statistical analysis of peptide microarrays
3 versions - Latest release: 6 months ago - 14.4 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 9.6% on bioconductor.org
CORREP 1.68.0
Multivariate Correlation Estimator and Statistical Inference Procedures.
3 versions - Latest release: 6 months ago - 28.8 thousand downloads total - 1 maintainer
Top 7.7% on bioconductor.org
rbsurv 2.60.0
Robust likelihood-based survival modeling with microarray data
3 versions - Latest release: 6 months ago - 30.9 thousand downloads total - 1 maintainer
cbaf 1.24.0
Automated functions for comparing various omic data from cbioportal.org
3 versions - Latest release: 6 months ago - 8.7 thousand downloads total - 1 maintainer
sigFeature 1.20.0
sigFeature: Significant feature selection using SVM-RFE & t-statistic
3 versions - Latest release: 6 months ago - 12.7 thousand downloads total - 1 maintainer
CCPROMISE 1.28.0
PROMISE analysis with Canonical Correlation for Two Forms of High Dimensional Genetic Data
3 versions - Latest release: 6 months ago - 9.68 thousand downloads total - 1 maintainer
arrayMvout 1.60.0
multivariate outlier detection for expression array QA
3 versions - Latest release: 6 months ago - 33.6 thousand downloads total - 1 maintainer
ExiMiR 2.44.0
R functions for the normalization of Exiqon miRNA array data
3 versions - Latest release: 6 months ago - 24.8 thousand downloads total - 1 maintainer
trigger 1.48.0
Transcriptional Regulatory Inference from Genetics of Gene ExpRession
3 versions - Latest release: 6 months ago - 22.3 thousand downloads total - 1 maintainer
Harman 1.30.0
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
3 versions - Latest release: 6 months ago - 1 dependent package - 20.4 thousand downloads total - 1 maintainer
miRspongeR 2.6.0
Identification and analysis of miRNA sponge regulation
3 versions - Latest release: 6 months ago - 1 dependent package - 6.08 thousand downloads total - 5 stars on GitHub - 1 maintainer
trio 3.40.0
Testing of SNPs and SNP Interactions in Case-Parent Trio Studies
3 versions - Latest release: 6 months ago - 23.7 thousand downloads total - 1 maintainer
MetaPhOR 1.4.0
Metabolic Pathway Analysis of RNA
3 versions - Latest release: 6 months ago - 1.67 thousand downloads total - 1 maintainer
Top 9.3% on bioconductor.org
spkTools 1.58.0
Methods for Spike-in Arrays
3 versions - Latest release: 6 months ago - 26 thousand downloads total - 1 maintainer
Top 6.2% on bioconductor.org
iClusterPlus 1.38.0
Integrative clustering of multi-type genomic data
3 versions - Latest release: 6 months ago - 1 dependent package - 48.8 thousand downloads total - 2 maintainers
Top 6.3% on bioconductor.org
gpls 1.74.0
Classification using generalized partial least squares
3 versions - Latest release: 6 months ago - 1 dependent package - 51.9 thousand downloads total - 1 maintainer
rifi 1.6.0
'rifi' analyses data from rifampicin time series created by microarray or RNAseq
3 versions - Latest release: 6 months ago - 1.71 thousand downloads total - 0 stars on GitHub - 1 maintainer
iGC 1.32.0
An integrated analysis package of Gene expression and Copy number alteration
3 versions - Latest release: 6 months ago - 11.3 thousand downloads total - 1 stars on GitHub - 1 maintainer
mimager 1.26.0
mimager: The Microarray Imager
3 versions - Latest release: 6 months ago - 9.09 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 8.8% on bioconductor.org
OLINgui 1.76.0
Graphical user interface for OLIN
3 versions - Latest release: 6 months ago - 28.6 thousand downloads total - 1 maintainer
Related Keywords
Software 374 GeneExpression 139 DifferentialExpression 121 Preprocessing 90 RNASeq 73 Sequencing 69 Visualization 64 QualityControl 61 OneChannel 58 ImmunoOncology 58 TwoChannel 52 MultipleComparison 49 Clustering 48 GeneSetEnrichment 41 DNAMethylation 39 Genetics 38 Transcription 38 DataImport 36 Classification 35 Normalization 33 Pathways 29 GraphAndNetwork 29 CopyNumberVariation 27 Proteomics 25 Network 24 MethylationArray 23 Regression 22 BatchEffect 22 Transcriptomics 21 GO 20 SNP 19 SystemsBiology 18 TimeCourse 18 StatisticalMethod 18 mRNAMicroarray 18 Annotation 16 Epigenetics 16 DifferentialMethylation 16 BiomedicalInformatics 16 ReportWriting 14 GeneRegulation 14 Bayesian 13 Metabolomics 12 ExonArray 11 GeneTarget 10 PrincipalComponent 10 r 9 Coverage 9 KEGG 9 FunctionalGenomics 9 Infrastructure 9 AlternativeSplicing 8 bioconductor 8 GeneticVariability 8 DifferentialSplicing 8 FeatureExtraction 8 ChIPSeq 8 ProprietaryPlatforms 8 NetworkInference 8 DataRepresentation 8 NetworkEnrichment 7 GUI 7 CpGIsland 7 SingleCell 7 bioconductor-package 6 MicroRNAArray 6 GenomeAnnotation 6 bioinformatics 6 DimensionReduction 6 MultiChannel 5 MethylSeq 5 GenePrediction 5 CellBiology 5 GenomeWideAssociation 5 GenomicVariation 4 genomics 4 ChIPchip 4 Spatial 4 WholeGenome 4 aCGH 4 TissueMicroarray 4 package 4 Reactome 3 Metagenomics 3 Alignment 3 GeneSignaling 3 DNASeq 3 SequenceMatching 3 Technology 3 Survival 3 MassSpectrometry 3 transcriptomics 3 ResearchField 3 Microbiome 2 AnnotationData 2 SAGE 2 Cheminformatics 2 FlowCytometry 2 differential-expression 2 MotifAnnotation 2