Ecosyste.ms: Packages

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

bioconductor.org "TwoChannel" keyword

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
Top 6.6% on bioconductor.org
methylumi 2.48.0
Handle Illumina methylation data
3 versions - Latest release: 6 months ago - 7 dependent packages - 296 thousand downloads total - 8 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
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 8.0% 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 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 8.9% on bioconductor.org
copa 1.70.0
Functions to perform cancer outlier profile analysis.
3 versions - Latest release: 6 months ago - 33 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
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
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
skewr 1.34.0
Visualize Intensities Produced by Illumina's Human Methylation 450k BeadChip
3 versions - Latest release: 6 months ago - 11.7 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 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
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
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
AMARETTO 1.18.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...
3 versions - Latest release: 6 months ago - 7.55 thousand downloads total - 1 maintainer
Top 8.3% on bioconductor.org
MANOR 1.74.0
CGH Micro-Array NORmalization
3 versions - Latest release: 6 months ago - 30.2 thousand downloads total - 1 maintainer
RegEnrich 1.12.1
Gene regulator enrichment analysis
4 versions - Latest release: about 1 month ago - 4.65 thousand downloads total - 1 maintainer
normalize450K 1.30.0
Preprocessing of Illumina Infinium 450K data
3 versions - Latest release: 6 months ago - 9.45 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
daMA 1.74.0
Efficient design and analysis of factorial two-colour microarray data
3 versions - Latest release: 6 months ago - 29.8 thousand downloads total - 1 maintainer
Top 9.3% on bioconductor.org
HELP 1.60.0
Tools for HELP data analysis
3 versions - Latest release: 6 months ago - 29.5 thousand downloads total - 1 maintainer
mCSEA 1.22.0
Methylated CpGs Set Enrichment Analysis
3 versions - Latest release: 6 months ago - 1 dependent package - 9.56 thousand downloads total - 1 maintainer
Top 8.4% on bioconductor.org
stepNorm 1.74.0
Stepwise normalization functions for cDNA microarrays
3 versions - Latest release: 6 months ago - 28.1 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
EGSEA 1.30.1
Ensemble of Gene Set Enrichment Analyses
4 versions - Latest release: 4 months ago - 1 dependent package - 28 thousand downloads total - 1 maintainer
Top 8.8% on bioconductor.org
SMAP 1.66.0
A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling
3 versions - Latest release: 6 months ago - 26.9 thousand downloads total - 1 maintainer
snapCGH 1.72.0 removed
Segmentation, normalisation and processing of aCGH data
2 versions - Latest release: 6 months ago - 2 dependent packages - 41.8 thousand downloads total - 1 maintainer
Top 6.2% on bioconductor.org
arrayQuality 1.80.0
Assessing array quality on spotted arrays
3 versions - Latest release: 6 months ago - 60.8 thousand downloads total - 1 maintainer
iCheck 1.32.0
QC Pipeline and Data Analysis Tools for High-Dimensional Illumina mRNA Expression Data
3 versions - Latest release: 6 months ago - 12.6 thousand downloads total - 1 maintainer
ENmix 1.38.01
Quality control and analysis tools for Illumina DNA methylation BeadChip
3 versions - Latest release: 6 months ago - 27.6 thousand downloads total - 1 maintainer
MSstatsLOBD 1.10.0
Assay characterization: estimation of limit of blanc(LoB) and limit of detection(LOD)
3 versions - Latest release: 6 months ago - 2.85 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 9.5% on bioconductor.org
beadarraySNP 1.68.0
Normalization and reporting of Illumina SNP bead arrays
3 versions - Latest release: 6 months ago - 37.6 thousand downloads total - 1 maintainer
TurboNorm 1.50.0
A fast scatterplot smoother suitable for microarray normalization
3 versions - Latest release: 6 months ago - 23 thousand downloads total - 1 maintainer
ARRmNormalization 1.42.0
Adaptive Robust Regression normalization for Illumina methylation data
3 versions - Latest release: 6 months ago - 21.5 thousand downloads total - 1 maintainer
Top 9.3% on bioconductor.org
dyebias 1.62.0
The GASSCO method for correcting for slide-dependent gene-specific dye bias
3 versions - Latest release: 6 months ago - 28.4 thousand downloads total - 1 maintainer
MSstatsPTM 2.4.4
Statistical Characterization of Post-translational Modifications
5 versions - Latest release: 3 months ago - 2 dependent packages - 7.43 thousand downloads total - 6 stars on GitHub - 1 maintainer
Top 1.9% on bioconductor.org
minfi 1.50.0
Analyze Illumina Infinium DNA methylation arrays
3 versions - Latest release: 20 days ago - 31 dependent packages - 788 thousand downloads total - 56 stars on GitHub - 1 maintainer
Top 1.8% on bioconductor.org
lumi 2.56.0
BeadArray Specific Methods for Illumina Methylation and Expression Microarrays
3 versions - Latest release: 16 days ago - 10 dependent packages - 335 thousand downloads total - 1 maintainer
cytomapper 1.16.0
Visualization of highly multiplexed imaging data in R
3 versions - Latest release: 7 days ago - 3 dependent packages - 14.1 thousand downloads total - 32 stars on GitHub - 1 maintainer
Top 1.4% on bioconductor.org
GEOquery 2.72.0
Get data from NCBI Gene Expression Omnibus (GEO)
3 versions - Latest release: 19 days ago - 47 dependent packages - 1.87 million downloads total - 82 stars on GitHub - 1 maintainer
Top 1.7% on bioconductor.org
vsn 3.72.0
Variance stabilization and calibration for microarray data
3 versions - Latest release: 19 days ago - 30 dependent packages - 893 thousand downloads total - 1 maintainer
Top 0.3% on bioconductor.org
limma 3.60.0
Linear Models for Microarray Data
4 versions - Latest release: 19 days ago - 322 dependent packages - 5.09 million downloads total - 1 maintainer
MSstatsLiP 1.10.0
LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments
5 versions - Latest release: 8 days ago - 2.64 thousand downloads total - 3 stars on GitHub - 1 maintainer
MSstatsShiny 1.6.0
MSstats GUI for Statistical Anaylsis of Proteomics Experiments
6 versions - Latest release: 10 days ago - 2.75 thousand downloads total - 9 stars on GitHub - 1 maintainer
Top 4.5% on bioconductor.org
ArrayExpress 1.64.0
Access the ArrayExpress Collection at EMBL-EBI Biostudies and build Bioconductor data structures:...
3 versions - Latest release: 12 days ago - 1 dependent package - 131 thousand downloads total - 1 maintainer
Top 3.8% on bioconductor.org
aroma.light 3.34.0
Light-Weight Methods for Normalization and Visualization of Microarray Data using Only Basic R Da...
3 versions - Latest release: 12 days ago - 3 dependent packages - 324 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 4.7% on bioconductor.org
RnBeads 2.22.0
RnBeads
3 versions - Latest release: 12 days ago - 1 dependent package - 54.4 thousand downloads total - 1 maintainer
Top 3.3% on bioconductor.org
DMRcate 3.0.0
Methylation array and sequencing spatial analysis methods
4 versions - Latest release: 12 days ago - 2 dependent packages - 135 thousand downloads total - 1 maintainer
Top 5.4% on bioconductor.org
limmaGUI 1.80.0
GUI for limma Package With Two Color Microarrays
3 versions - Latest release: 13 days ago - 48.9 thousand downloads total - 1 maintainer
Top 5.3% on bioconductor.org
puma 3.46.0
Propagating Uncertainty in Microarray Analysis(including Affymetrix tranditional 3' arrays and ex...
3 versions - Latest release: 13 days ago - 1 dependent package - 46.1 thousand downloads total - 1 maintainer
Top 3.2% on bioconductor.org
oligo 1.68.0
Preprocessing tools for oligonucleotide arrays
3 versions - Latest release: 13 days ago - 11 dependent packages - 368 thousand downloads total - 1 maintainer
Top 4.3% on bioconductor.org
ChAMP 2.34.0
Chip Analysis Methylation Pipeline for Illumina HumanMethylation450 and EPIC
3 versions - Latest release: 13 days ago - 1 dependent package - 117 thousand downloads total - 1 maintainer
Top 3.5% on bioconductor.org
Ringo 1.66.0 removed
R Investigation of ChIP-chip Oligoarrays
2 versions - Latest release: 6 months ago - 2 dependent packages - 86.1 thousand downloads total - 1 maintainer
Top 5.4% on bioconductor.org
wateRmelon 2.10.0
Illumina 450 and EPIC methylation array normalization and metrics
3 versions - Latest release: 13 days ago - 5 dependent packages - 132 thousand downloads total - 1 maintainer
Top 4.5% on bioconductor.org
convert 1.80.0
Convert Microarray Data Objects
3 versions - Latest release: 13 days ago - 4 dependent packages - 69.5 thousand downloads total - 1 maintainer
Top 4.3% on bioconductor.org
arrayQualityMetrics 3.60.0
Quality metrics report for microarray data sets
3 versions - Latest release: 13 days ago - 181 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 3.0% on bioconductor.org
gage 2.54.0
Generally Applicable Gene-set Enrichment for Pathway Analysis
3 versions - Latest release: 20 days ago - 4 dependent packages - 171 thousand downloads total - 5 stars on GitHub - 1 maintainer
roastgsa 1.0.0
Rotation based gene set analysis
1 version - Latest release: 7 months ago - 569 downloads total - 0 stars on GitHub - 1 maintainer
shinyMethyl 1.38.0
Interactive visualization for Illumina methylation arrays
2 versions - Latest release: 6 months ago - 23.6 thousand downloads total - 3 stars on GitHub - 1 maintainer
diffcoexp 1.22.0
Differential Co-expression Analysis
2 versions - Latest release: 6 months ago - 10.4 thousand downloads total - 15 stars on GitHub - 1 maintainer
REMP 1.26.0
Repetitive Element Methylation Prediction
2 versions - Latest release: 6 months ago - 10.7 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 2.2% on bioconductor.org
marray 1.80.0
Exploratory analysis for two-color spotted microarray data
2 versions - Latest release: 7 months ago - 21 dependent packages - 547 thousand downloads total - 1 maintainer
MAGAR 1.10.0
MAGAR: R-package to compute methylation Quantitative Trait Loci (methQTL) from DNA methylation an...
2 versions - Latest release: 6 months ago - 3.97 thousand downloads total - 0 stars on GitHub - 1 maintainer
cytoviewer 1.2.0
An interactive multi-channel image viewer for R
2 versions - Latest release: 7 months ago - 1.7 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 6.5% on bioconductor.org
PADOG 1.44.0
Pathway Analysis with Down-weighting of Overlapping Genes (PADOG)
2 versions - Latest release: 6 months ago - 2 dependent packages - 38.8 thousand downloads total - 1 maintainer
Related Keywords
Software 64 Microarray 52 Preprocessing 40 QualityControl 32 OneChannel 31 DataImport 21 DifferentialExpression 21 DNAMethylation 20 ImmunoOncology 16 Normalization 15 GeneExpression 14 MethylationArray 14 MultipleComparison 10 Sequencing 10 Epigenetics 9 DifferentialMethylation 8 RNASeq 8 Visualization 8 BatchEffect 8 Proteomics 7 Transcription 7 CopyNumberVariation 6 Regression 6 GeneSetEnrichment 6 MultiChannel 6 ExonArray 6 mRNAMicroarray 6 Clustering 6 CpGIsland 6 TimeCourse 5 Genetics 5 Bayesian 5 DifferentialSplicing 4 Network 4 AlternativeSplicing 4 MassSpectrometry 4 SystemsBiology 4 r 3 bioconductor 3 SNP 3 GUI 3 Pathways 3 Metabolomics 3 GraphAndNetwork 3 Transcriptomics 3 ProprietaryPlatforms 3 MicroRNAArray 3 MethylSeq 2 SingleCell 2 Coverage 2 GeneticVariability 2 proteomics 2 Infrastructure 2 FunctionalGenomics 2 Cheminformatics 2 CellBiology 2 BiomedicalInformatics 2 GO 2 GenomeAnnotation 2 Classification 2 GeneTarget 2 NetworkEnrichment 2 ShinyApps 1 rstats 1 package 1 visualization 1 WholeGenome 1 shiny 1 ChipOnChip 1 imaging 1 Spatial 1 GenomeWideAssociation 1 Survival 1 HTA2.0 1 CopyNumber 1 ReportWriting 1 GeneRegulation 1 ExperimentData 1 StatisticalMethod 1 Cancer 1 ThirdPartyClient 1 FunctionalPrediction 1 NetworkInference 1 GeneSignaling 1 KEGG 1 PrincipalComponent 1 mass-spectrometry 1 post-translational-modification 1 bioimaging 1 imaging-mass-cytometry 1 single-cell 1 spatial-analysis 1 SAGE 1 bioinformatics 1 data-science 1 genomics 1 ncbi-geo 1