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 Consensus1 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
6 versions - Latest release: 30 days ago - 27 dependent packages - 1.25 million downloads total - 1 maintainer
DOSE 3.30.0
Disease Ontology Semantic and Enrichment analysis6 versions - Latest release: 30 days ago - 27 dependent packages - 1.25 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
4 versions - Latest release: 30 days ago - 59 dependent packages - 1.41 million downloads total - 1 maintainer
clusterProfiler 4.12.0
A universal enrichment tool for interpreting omics data4 versions - Latest release: 30 days ago - 59 dependent packages - 1.41 million downloads total - 1 maintainer
Top 0.6% on bioconductor.org
14 versions - Latest release: 30 days ago - 181 dependent packages - 3.03 million downloads total - 4 maintainers
edgeR 4.2.0
Empirical Analysis of Digital Gene Expression Data in R14 versions - Latest release: 30 days ago - 181 dependent packages - 3.03 million downloads total - 4 maintainers
Top 0.3% on bioconductor.org
5 versions - Latest release: 30 days ago - 322 dependent packages - 5.11 million downloads total - 1 maintainer
limma 3.60.0
Linear Models for Microarray Data5 versions - Latest release: 30 days ago - 322 dependent packages - 5.11 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
3 versions - Latest release: 30 days ago - 37 dependent packages - 2.02 million downloads total - 1 maintainer
multtest 2.60.0
Resampling-based multiple hypothesis testing3 versions - Latest release: 30 days ago - 37 dependent packages - 2.02 million downloads total - 1 maintainer
Top 1.7% on bioconductor.org
3 versions - Latest release: 30 days ago - 43 dependent packages - 808 thousand downloads total - 3 maintainers
sva 3.52.0
Surrogate Variable Analysis3 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 analyses3 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 tests4 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 motifs3 versions - Latest release: 7 months ago - 12.8 thousand downloads total - 7 stars on GitHub
Top 4.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 15 dependent packages - 399 thousand downloads total - 15 stars on GitHub - 1 maintainer
bumphunter 1.44.0
Bump Hunter3 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 hotspots2 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 App3 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 analysis2 versions - Latest release: 7 months ago - 881 downloads total - 0 stars on GitHub - 1 maintainer
Top 2.3% on bioconductor.org
3 versions - Latest release: 7 months ago - 23 dependent packages - 504 thousand downloads total - 1 maintainer
GOstats 2.68.0
Tools for manipulating GO and microarrays3 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 annotations3 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 data3 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 information3 versions - Latest release: 6 months ago - 16.5 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 2.8% on bioconductor.org
3 versions - Latest release: 7 months ago - 15 dependent packages - 443 thousand downloads total - 1 maintainer
ReactomePA 1.46.0
Reactome Pathway Analysis3 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 Controls3 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 plots3 versions - Latest release: 6 months ago - 6.99 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 2.1% on bioconductor.org
3 versions - Latest release: 7 months ago - 23 dependent packages - 696 thousand downloads total - 1 maintainer
phyloseq 1.46.0
Handling and analysis of high-throughput microbiome census data3 versions - Latest release: 7 months ago - 23 dependent packages - 696 thousand downloads total - 1 maintainer
calm 1.16.0
Covariate Assisted Large-scale Multiple testing3 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 Selection3 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 Data3 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 Datasets9 versions - Latest release: about 2 months ago - 2.13 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 3.8% on bioconductor.org
3 versions - Latest release: 7 months ago - 6 dependent packages - 434 thousand downloads total - 1 maintainer
siggenes 1.76.0
Multiple Testing using SAM and Efron's Empirical Bayes Approaches3 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 control3 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 markers3 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 plots3 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 mice3 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 analysis3 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 data6 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 annotations3 versions - Latest release: 7 months ago - 23.7 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 7.0% on bioconductor.org
3 versions - Latest release: 7 months ago - 32.8 thousand downloads total - 1 maintainer
SpeCond 1.56.0
Condition specific detection from expression data3 versions - Latest release: 7 months ago - 32.8 thousand downloads total - 1 maintainer
twilight 1.78.0
Estimation of local false discovery rate3 versions - Latest release: 7 months ago - 1 dependent package - 45 thousand downloads total - 1 maintainer
microbiomeExplorer 1.12.0
Microbiome Exploration App3 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 libraries3 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 distribution3 versions - Latest release: 7 months ago - 16.9 thousand downloads total - 1 maintainer
Clomial 1.38.0
Infers clonal composition of a tumor3 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 Spectrometry3 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 Variants3 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 sets3 versions - Latest release: 7 months ago - 21.6 thousand downloads total - 1 maintainer
rexposome 1.24.1
Exposome exploration and outcome data analysis3 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 analysis3 versions - Latest release: 7 months ago - 10 thousand downloads total - 1 maintainer
MineICA 1.42.0
Analysis of an ICA decomposition obtained on genomics data3 versions - Latest release: 7 months ago - 21.5 thousand downloads total - 1 maintainer
Top 7.7% on bioconductor.org
3 versions - Latest release: 7 months ago - 37.4 thousand downloads total - 1 maintainer
CGEN 3.38.0
An R package for analysis of case-control studies in genetic epidemiology3 versions - Latest release: 7 months ago - 37.4 thousand downloads total - 1 maintainer
ISoLDE 1.30.0
Integrative Statistics of alleLe Dependent Expression3 versions - Latest release: 7 months ago - 9.18 thousand downloads total - 1 maintainer
cydar 1.26.0
Using Mass Cytometry for Differential Abundance Analyses3 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 surfaltr3 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 distributions3 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
3 versions - Latest release: 24 days ago - 6 dependent packages - 123 thousand downloads total - 0 stars on GitHub - 1 maintainer
baySeq 2.38.0
Empirical Bayesian analysis of patterns of differential expression in count data3 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
3 versions - Latest release: 7 months ago - 34.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
segmentSeq 2.36.0
Methods for identifying small RNA loci from high-throughput sequencing data3 versions - Latest release: 7 months ago - 34.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 7.6% on bioconductor.org
3 versions - Latest release: 7 months ago - 32.6 thousand downloads total - 1 maintainer
Mulcom 1.52.0
Calculates Mulcom test3 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 data3 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 analysis3 versions - Latest release: 7 months ago - 6.96 thousand downloads total - 1 maintainer
omicade4 1.42.0
Multiple co-inertia analysis of omics datasets3 versions - Latest release: 7 months ago - 5 dependent packages - 24.7 thousand downloads total - 1 maintainer
Top 7.9% on bioconductor.org
3 versions - Latest release: 7 months ago - 3 dependent packages - 32.9 thousand downloads total - 1 maintainer
quantro 1.36.0
A test for when to use quantile normalization3 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 graph3 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 Data3 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 Sequencing4 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 Tissue3 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 profiles3 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 normalization3 versions - Latest release: 7 months ago - 7.31 thousand downloads total - 1 maintainer
Top 7.6% on bioconductor.org
3 versions - Latest release: 7 months ago - 1 dependent package - 38.5 thousand downloads total - 1 maintainer
DRIMSeq 1.30.0
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq3 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 Sets3 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 Data3 versions - Latest release: 7 months ago - 9.28 thousand downloads total - 1 maintainer
snm 1.50.0
Supervised Normalization of Microarrays3 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 phenoTypes3 versions - Latest release: 7 months ago - 11.8 thousand downloads total - 1 maintainer
R4RNA 1.30.0
An R package for RNA visualization and analysis3 versions - Latest release: 7 months ago - 2 dependent packages - 30 thousand downloads total - 1 maintainer
openPrimeR 1.24.0
Multiplex PCR Primer Design and Analysis3 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 binding3 versions - Latest release: 7 months ago - 3.5 thousand downloads total - 1 maintainer
edge 2.34.0
Extraction of Differential Gene Expression3 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 subtypes3 versions - Latest release: 7 months ago - 1 dependent package - 22 thousand downloads total - 1 maintainer
Top 8.4% on bioconductor.org
3 versions - Latest release: 7 months ago - 1 dependent package - 32.2 thousand downloads total - 1 maintainer
gaga 2.48.0
GaGa hierarchical model for high-throughput data analysis3 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 technique3 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 Analysis3 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 alteration3 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 data4 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 patterns3 versions - Latest release: 7 months ago - 8.96 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 7.7% on bioconductor.org
3 versions - Latest release: 7 months ago - 1 dependent package - 38.4 thousand downloads total - 1 maintainer
GeneOverlap 1.38.0
Test and visualize gene overlaps3 versions - Latest release: 7 months ago - 1 dependent package - 38.4 thousand downloads total - 1 maintainer
Top 6.5% on bioconductor.org
3 versions - Latest release: 7 months ago - 1 dependent package - 38.4 thousand downloads total - 1 maintainer
parody 1.60.0
Parametric And Resistant Outlier DYtection3 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 MSKCC6 versions - Latest release: about 1 month ago - 19 thousand downloads total - 8 stars on GitHub - 1 maintainer
Top 6.5% on bioconductor.org
3 versions - Latest release: 7 months ago - 1 dependent package - 41.8 thousand downloads total - 1 maintainer
goProfiles 1.64.0
goProfiles: an R package for the statistical analysis of functional profiles3 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 information3 versions - Latest release: 7 months ago - 20.3 thousand downloads total - 1 maintainer
Top 7.3% on bioconductor.org
3 versions - Latest release: 7 months ago - 32.8 thousand downloads total - 1 maintainer
RBioinf 1.62.0
RBioinf3 versions - Latest release: 7 months ago - 32.8 thousand downloads total - 1 maintainer
regioneReloaded 1.4.0
RegioneReloaded: Multiple Association for Genomic Region Sets3 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