Ecosyste.ms: Packages

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

bioconductor.org "MultipleComparison" keyword

dar 1.0.0
Differential Abundance Analysis by Consensus
1 version - Latest release: about 1 month ago - 335 downloads total - 1 stars on GitHub - 1 maintainer
betaHMM 1.0.0
A Hidden Markov Model Approach for Identifying Differentially Methylated Sites and Regions for Be...
1 version - Latest release: about 1 month ago - 378 downloads total - 1 maintainer
Top 1.6% on bioconductor.org
DOSE 3.30.0
Disease Ontology Semantic and Enrichment analysis
6 versions - Latest release: 30 days ago - 27 dependent packages - 1.25 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
clusterProfiler 4.12.0
A universal enrichment tool for interpreting omics data
4 versions - Latest release: 30 days ago - 59 dependent packages - 1.41 million downloads total - 1 maintainer
Top 0.6% on bioconductor.org
edgeR 4.2.0
Empirical Analysis of Digital Gene Expression Data in R
14 versions - Latest release: 30 days ago - 181 dependent packages - 3.03 million downloads total - 4 maintainers
Top 0.3% on bioconductor.org
limma 3.60.0
Linear Models for Microarray Data
5 versions - Latest release: 30 days ago - 322 dependent packages - 5.11 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
multtest 2.60.0
Resampling-based multiple hypothesis testing
3 versions - Latest release: 30 days ago - 37 dependent packages - 2.02 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
sva 3.52.0
Surrogate Variable Analysis
3 versions - Latest release: 30 days ago - 43 dependent packages - 808 thousand downloads total - 3 maintainers
QUBIC 1.30.0
An R package for qualitative biclustering in support of gene co-expression analyses
3 versions - Latest release: 6 months ago - 2 dependent packages - 25.2 thousand downloads total - 3 stars on GitHub - 1 maintainer
distinct 1.14.5
distinct: a method for differential analyses via hierarchical permutation tests
4 versions - Latest release: 5 months ago - 2 dependent packages - 8.74 thousand downloads total - 11 stars on GitHub - 1 maintainer
DiffLogo 2.26.0
DiffLogo: A comparative visualisation of biooligomer motifs
3 versions - Latest release: 7 months ago - 12.8 thousand downloads total - 7 stars on GitHub
Top 4.7% on bioconductor.org
bumphunter 1.44.0
Bump Hunter
3 versions - Latest release: 6 months ago - 15 dependent packages - 399 thousand downloads total - 15 stars on GitHub - 1 maintainer
limpca 1.0.0
An R package for the linear modeling of high-dimensional designed data based on ASCA/APCA family ...
1 version - Latest release: about 1 month ago - 192 downloads total - 0 stars on GitHub - 1 maintainer
compSPOT 1.0.0
compSPOT: Tool for identifying and comparing significantly mutated genomic hotspots
2 versions - Latest release: 7 months ago - 899 downloads total - 0 stars on GitHub - 1 maintainer
ChromSCape 1.12.0
Analysis of single-cell epigenomics datasets with a Shiny App
3 versions - Latest release: 7 months ago - 4.34 thousand downloads total - 14 stars on GitHub - 1 maintainer
roastgsa 1.0.0
Rotation based gene set analysis
2 versions - Latest release: 7 months ago - 881 downloads total - 0 stars on GitHub - 1 maintainer
Top 2.3% on bioconductor.org
GOstats 2.68.0
Tools for manipulating GO and microarrays
3 versions - Latest release: 7 months ago - 23 dependent packages - 504 thousand downloads total - 1 maintainer
GOexpress 1.36.0
Visualise microarray and RNAseq data using gene ontology annotations
3 versions - Latest release: 6 months ago - 1 dependent package - 24.2 thousand downloads total - 9 stars on GitHub - 1 maintainer
swfdr 1.28.0
Estimation of the science-wise false discovery rate and the false discovery rate conditional on c...
3 versions - Latest release: 7 months ago - 8.74 thousand downloads total - 3 stars on GitHub - 2 maintainers
FindIT2 1.8.0
find influential TF and Target based on multi-omics data
3 versions - Latest release: 7 months ago - 2.77 thousand downloads total - 6 stars on GitHub - 1 maintainer
OPWeight 1.24.0
Optimal p-value weighting with independent information
3 versions - Latest release: 6 months ago - 16.5 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 2.8% on bioconductor.org
ReactomePA 1.46.0
Reactome Pathway Analysis
3 versions - Latest release: 7 months ago - 15 dependent packages - 443 thousand downloads total - 1 maintainer
erccdashboard 1.36.0
Assess Differential Gene Expression Experiments with ERCC Controls
3 versions - Latest release: 6 months ago - 19 thousand downloads total - 7 stars on GitHub - 1 maintainer
metagene2 1.18.0
A package to produce metagene plots
3 versions - Latest release: 6 months ago - 6.99 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
phyloseq 1.46.0
Handling and analysis of high-throughput microbiome census data
3 versions - Latest release: 7 months ago - 23 dependent packages - 696 thousand downloads total - 1 maintainer
calm 1.16.0
Covariate Assisted Large-scale Multiple testing
3 versions - Latest release: 6 months ago - 4.59 thousand downloads total - 0 stars on GitHub - 1 maintainer
pathwayPCA 1.18.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
3 versions - Latest release: 6 months ago - 1 dependent package - 7.56 thousand downloads total - 11 stars on GitHub - 1 maintainer
chromstaR 1.28.0
Combinatorial and Differential Chromatin State Analysis for ChIP-Seq Data
3 versions - Latest release: 6 months ago - 14.1 thousand downloads total - 7 stars on GitHub - 1 maintainer
EpiCompare 1.6.7
Comparison, Benchmarking & QC of Epigenomic Datasets
9 versions - Latest release: about 2 months ago - 2.13 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
siggenes 1.76.0
Multiple Testing using SAM and Efron's Empirical Bayes Approaches
3 versions - Latest release: 7 months ago - 6 dependent packages - 434 thousand downloads total - 1 maintainer
tripr 1.8.0
T-cell Receptor/Immunoglobulin Profiler (TRIP)
3 versions - Latest release: 7 months ago - 2.64 thousand downloads total - 2 stars on GitHub - 1 maintainer
onlineFDR 2.10.0
Online error rate control
3 versions - Latest release: 6 months ago - 5.69 thousand downloads total - 13 stars on GitHub - 1 maintainer
OVESEG 1.18.0
OVESEG-test to detect tissue/cell-specific markers
3 versions - Latest release: 6 months ago - 5.29 thousand downloads total - 1 stars on GitHub - 1 maintainer
metagene 2.34.0
A package to produce metagene plots
3 versions - Latest release: 6 months ago - 17.6 thousand downloads total - 11 stars on GitHub - 1 maintainer
MouseFM 1.12.0
In-silico methods for genetic finemapping in inbred mice
3 versions - Latest release: 6 months ago - 5.37 thousand downloads total - 0 stars on GitHub - 1 maintainer
plotGrouper 1.20.0
Shiny app GUI wrapper for ggplot with built-in statistical analysis
3 versions - Latest release: 6 months ago - 6.22 thousand downloads total - 7 stars on GitHub - 1 maintainer
DifferentialRegulation 2.0.3
Differentially regulated genes from scRNA-seq data
6 versions - Latest release: 3 months ago - 2.37 thousand downloads total - 8 stars on GitHub - 1 maintainer
categoryCompare 1.46.0
Meta-analysis of high-throughput experiments using feature annotations
3 versions - Latest release: 7 months ago - 23.7 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 7.0% on bioconductor.org
SpeCond 1.56.0
Condition specific detection from expression data
3 versions - Latest release: 7 months ago - 32.8 thousand downloads total - 1 maintainer
twilight 1.78.0
Estimation of local false discovery rate
3 versions - Latest release: 7 months ago - 1 dependent package - 45 thousand downloads total - 1 maintainer
microbiomeExplorer 1.12.0
Microbiome Exploration App
3 versions - Latest release: 7 months ago - 6.29 thousand downloads total - 1 maintainer
abseqR 1.20.0
Reporting and data analysis functionalities for Rep-Seq datasets of antibody libraries
3 versions - Latest release: 7 months ago - 7.28 thousand downloads total - 0 stars on GitHub - 1 maintainer
bacon 1.30.0
Controlling bias and inflation in association studies using the empirical null distribution
3 versions - Latest release: 7 months ago - 16.9 thousand downloads total - 1 maintainer
Clomial 1.38.0
Infers clonal composition of a tumor
3 versions - Latest release: 7 months ago - 16.4 thousand downloads total - 1 maintainer
IsoformSwitchAnalyzeR 2.2.0
Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- a...
3 versions - Latest release: 7 months ago - 28.3 thousand downloads total - 1 maintainer
artMS 1.20.0
Analytical R tools for Mass Spectrometry
3 versions - Latest release: 7 months ago - 9.23 thousand downloads total - 1 maintainer
satuRn 1.10.0
Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applic...
3 versions - Latest release: 7 months ago - 1 dependent package - 7.57 thousand downloads total - 20 stars on GitHub - 1 maintainer
cnvGSA 1.46.0
Gene Set Analysis of (Rare) Copy Number Variants
3 versions - Latest release: 7 months ago - 22.7 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: 7 months ago - 21.6 thousand downloads total - 1 maintainer
rexposome 1.24.1
Exposome exploration and outcome data analysis
3 versions - Latest release: 7 months ago - 1 dependent package - 10.3 thousand downloads total - 1 maintainer
GGPA 1.14.0
graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architec...
3 versions - Latest release: 7 months ago - 4.23 thousand downloads total - 1 stars on GitHub - 1 maintainer
OMICsPCA 1.20.0
An R package for quantitative integration and analysis of multiple omics assays from heterogeneou...
3 versions - Latest release: 7 months ago - 7.29 thousand downloads total - 1 maintainer
MetaNeighbor 1.22.0
Single cell replicability analysis
3 versions - Latest release: 7 months ago - 10 thousand downloads total - 1 maintainer
MineICA 1.42.0
Analysis of an ICA decomposition obtained on genomics data
3 versions - Latest release: 7 months ago - 21.5 thousand downloads total - 1 maintainer
Top 7.7% on bioconductor.org
CGEN 3.38.0
An R package for analysis of case-control studies in genetic epidemiology
3 versions - Latest release: 7 months ago - 37.4 thousand downloads total - 1 maintainer
ISoLDE 1.30.0
Integrative Statistics of alleLe Dependent Expression
3 versions - Latest release: 7 months ago - 9.18 thousand downloads total - 1 maintainer
cydar 1.26.0
Using Mass Cytometry for Differential Abundance Analyses
3 versions - Latest release: 7 months ago - 13.2 thousand downloads total - 1 maintainer
surfaltr 1.8.0
Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr
3 versions - Latest release: 7 months ago - 2.28 thousand downloads total - 1 maintainer
scDD 1.26.0
Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions
3 versions - Latest release: 7 months ago - 1 dependent package - 19.2 thousand downloads total - 32 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
baySeq 2.38.0
Empirical Bayesian analysis of patterns of differential expression in count data
3 versions - Latest release: 24 days ago - 6 dependent packages - 123 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 6.7% on bioconductor.org
segmentSeq 2.36.0
Methods for identifying small RNA loci from high-throughput sequencing data
3 versions - Latest release: 7 months ago - 34.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 7.6% on bioconductor.org
Mulcom 1.52.0
Calculates Mulcom test
3 versions - Latest release: 7 months ago - 32.6 thousand downloads total - 1 maintainer
LinkHD 1.16.0
LinkHD: a versatile framework to explore and integrate heterogeneous data
3 versions - Latest release: 7 months ago - 4.84 thousand downloads total - 1 maintainer
geva 1.10.0
Gene Expression Variation Analysis (GEVA)
3 versions - Latest release: 7 months ago - 2.79 thousand downloads total - 2 stars on GitHub - 1 maintainer
TTMap 1.24.0
Two-Tier Mapper: a clustering tool based on topological data analysis
3 versions - Latest release: 7 months ago - 6.96 thousand downloads total - 1 maintainer
omicade4 1.42.0
Multiple co-inertia analysis of omics datasets
3 versions - Latest release: 7 months ago - 5 dependent packages - 24.7 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: 7 months ago - 3 dependent packages - 32.9 thousand downloads total - 1 maintainer
miloR 2.0.0
Differential neighbourhood abundance testing on a graph
3 versions - Latest release: about 1 month ago - 10.9 thousand downloads total - 310 stars on GitHub - 1 maintainer
diffHic 1.34.0
Differential Analysis of Hi-C Data
3 versions - Latest release: 7 months ago - 22.9 thousand downloads total - 3 maintainers
dmrseq 1.22.1
Detection and inference of differentially methylated regions from Whole Genome Bisulfite Sequencing
4 versions - Latest release: 2 months ago - 1 dependent package - 17.9 thousand downloads total - 1 maintainer
SimFFPE 1.14.0
NGS Read Simulator for FFPE Tissue
3 versions - Latest release: 7 months ago - 4.18 thousand downloads total - 1 maintainer
similaRpeak 1.34.0
Metrics to estimate a level of similarity between two ChIP-Seq profiles
3 versions - Latest release: 7 months ago - 1 dependent package - 14 thousand downloads total - 7 stars on GitHub - 1 maintainer
GPA 1.14.0
GPA (Genetic analysis incorporating Pleiotropy and Annotation)
3 versions - Latest release: 7 months ago - 4.2 thousand downloads total - 8 stars on GitHub - 1 maintainer
qsmooth 1.18.0
Smooth quantile normalization
3 versions - Latest release: 7 months ago - 7.31 thousand downloads total - 1 maintainer
Top 7.6% on bioconductor.org
DRIMSeq 1.30.0
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
3 versions - Latest release: 7 months ago - 1 dependent package - 38.5 thousand downloads total - 1 maintainer
CoGAPS 3.22.0
Coordinated Gene Activity in Pattern Sets
3 versions - Latest release: 7 months ago - 3 dependent packages - 29.2 thousand downloads total - 4 maintainers
IWTomics 1.26.0
Interval-Wise Testing for Omics Data
3 versions - Latest release: 7 months ago - 9.28 thousand downloads total - 1 maintainer
snm 1.50.0
Supervised Normalization of Microarrays
3 versions - Latest release: 7 months ago - 1 dependent package - 35.5 thousand downloads total - 1 maintainer
SIAMCAT 2.6.0
Statistical Inference of Associations between Microbial Communities And host phenoTypes
3 versions - Latest release: 7 months ago - 11.8 thousand downloads total - 1 maintainer
R4RNA 1.30.0
An R package for RNA visualization and analysis
3 versions - Latest release: 7 months ago - 2 dependent packages - 30 thousand downloads total - 1 maintainer
openPrimeR 1.24.0
Multiplex PCR Primer Design and Analysis
3 versions - Latest release: 7 months ago - 1 dependent package - 13.1 thousand downloads total - 1 maintainer
nearBynding 1.12.0
Discern RNA structure proximal to protein binding
3 versions - Latest release: 7 months ago - 3.5 thousand downloads total - 1 maintainer
edge 2.34.0
Extraction of Differential Gene Expression
3 versions - Latest release: 7 months ago - 22.2 thousand downloads total - 20 stars on GitHub - 2 maintainers
ASSET 2.20.0
An R package for subset-based association analysis of heterogeneous traits and subtypes
3 versions - Latest release: 7 months ago - 1 dependent package - 22 thousand downloads total - 1 maintainer
Top 8.4% on bioconductor.org
gaga 2.48.0
GaGa hierarchical model for high-throughput data analysis
3 versions - Latest release: 7 months ago - 1 dependent package - 32.2 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: 7 months ago - 1 dependent package - 20.4 thousand downloads total - 1 maintainer
ERSSA 1.20.0
Empirical RNA-seq Sample Size Analysis
3 versions - Latest release: 7 months ago - 6.38 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: 7 months ago - 11.3 thousand downloads total - 1 stars on GitHub - 1 maintainer
AMARETTO 1.18.0
Regulatory Network Inference and Driver Gene Evaluation using Integrative Multi-Omics Analysis an...
3 versions - Latest release: 7 months ago - 7.55 thousand downloads total - 1 maintainer
bambu 3.4.1
Context-Aware Transcript Quantification from Long Read RNA-Seq data
4 versions - Latest release: about 1 month ago - 1 dependent package - 13 thousand downloads total - 118 stars on GitHub - 1 maintainer
clusterSeq 1.26.0
Clustering of high-throughput sequencing data by identifying co-expression patterns
3 versions - Latest release: 7 months ago - 8.96 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 7.7% on bioconductor.org
GeneOverlap 1.38.0
Test and visualize gene overlaps
3 versions - Latest release: 7 months ago - 1 dependent package - 38.4 thousand downloads total - 1 maintainer
Top 6.5% on bioconductor.org
parody 1.60.0
Parametric And Resistant Outlier DYtection
3 versions - Latest release: 7 months ago - 1 dependent package - 38.4 thousand downloads total - 1 maintainer
canceR 1.36.8
A Graphical User Interface for accessing and modeling the Cancer Genomics Data of MSKCC
6 versions - Latest release: about 1 month ago - 19 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 6.5% on bioconductor.org
goProfiles 1.64.0
goProfiles: an R package for the statistical analysis of functional profiles
3 versions - Latest release: 7 months ago - 1 dependent package - 41.8 thousand downloads total - 1 maintainer
goSorensen 1.4.0
Statistical inference based on the Sorensen-Dice dissimilarity and the Gene Ontology (GO)
3 versions - Latest release: 7 months ago - 1.75 thousand downloads total - 1 maintainer
flowMap 1.40.0
Mapping cell populations in flow cytometry data for cross-sample comparisons using the Friedman-R...
3 versions - Latest release: 7 months ago - 18.1 thousand downloads total - 1 maintainer
PathNet 1.42.0
An R package for pathway analysis using topological information
3 versions - Latest release: 7 months ago - 20.3 thousand downloads total - 1 maintainer
Top 7.3% on bioconductor.org
RBioinf 1.62.0
RBioinf
3 versions - Latest release: 7 months ago - 32.8 thousand downloads total - 1 maintainer
regioneReloaded 1.4.0
RegioneReloaded: Multiple Association for Genomic Region Sets
3 versions - Latest release: 7 months ago - 1.61 thousand downloads total - 5 stars on GitHub - 1 maintainer
Related Keywords
Software 183 DifferentialExpression 75 GeneExpression 67 Sequencing 64 ImmunoOncology 55 Visualization 51 Clustering 50 Microarray 49 RNASeq 42 Genetics 34 Normalization 31 Transcription 29 Preprocessing 29 Regression 28 GeneSetEnrichment 25 DataImport 25 Classification 24 QualityControl 24 StatisticalMethod 23 Transcriptomics 22 Annotation 21 Proteomics 20 Bayesian 20 SingleCell 20 Pathways 18 ChIPSeq 18 BatchEffect 18 BiomedicalInformatics 16 TimeCourse 16 FunctionalGenomics 16 Epigenetics 16 Coverage 15 SystemsBiology 14 GO 14 AlternativeSplicing 13 Alignment 13 DifferentialSplicing 13 bioconductor 13 OneChannel 12 SNP 12 DataRepresentation 11 r 10 Metabolomics 10 TwoChannel 10 Metagenomics 9 Microbiome 9 GUI 9 GeneticVariability 9 DNAMethylation 9 DifferentialMethylation 9 CellBiology 9 GeneTarget 8 DifferentialPeakCalling 8 mRNAMicroarray 8 ExonArray 7 KEGG 7 PrincipalComponent 7 DimensionReduction 7 FeatureExtraction 7 GenomeWideAssociation 7 GeneRegulation 6 ReportWriting 6 ATACSeq 6 FlowCytometry 6 GenomicVariation 5 GenePrediction 5 MethylationArray 5 GraphAndNetwork 5 MassSpectrometry 5 BiologicalQuestion 5 GenomeAnnotation 5 Reactome 5 WholeGenome 5 DNASeq 5 ExperimentalDesign 5 bioconductor-package 5 ProprietaryPlatforms 5 Network 5 Survival 4 MicrotitrePlateAssay 4 MicroRNAArray 4 PeakDetection 4 MethylSeq 4 bioinformatics 4 CopyNumberVariation 4 WorkflowStep 4 HiddenMarkovModel 3 rstats 3 microbiome 3 HistoneModification 3 gene-expression 3 MultipleSequenceAlignment 3 FunctionalPrediction 3 shiny 3 Technology 3 SequenceMatching 3 SAGE 3 Infrastructure 3 TargetedResequencing 2 cancer 2