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
microbiomeExplorer 1.12.0
Microbiome Exploration App3 versions - Latest release: 6 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: 6 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: 6 months ago - 16.9 thousand downloads total - 1 maintainer
Clomial 1.38.0
Infers clonal composition of a tumor3 versions - Latest release: 6 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: 6 months ago - 28.3 thousand downloads total - 1 maintainer
artMS 1.20.0
Analytical R tools for Mass Spectrometry3 versions - Latest release: 6 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: 6 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: 6 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: 6 months ago - 21.6 thousand downloads total - 1 maintainer
rexposome 1.24.1
Exposome exploration and outcome data analysis3 versions - Latest release: 6 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: 6 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: 6 months ago - 7.29 thousand downloads total - 1 maintainer
MetaNeighbor 1.22.0
Single cell replicability analysis3 versions - Latest release: 6 months ago - 10 thousand downloads total - 1 maintainer
MineICA 1.42.0
Analysis of an ICA decomposition obtained on genomics data3 versions - Latest release: 6 months ago - 21.5 thousand downloads total - 1 maintainer
Top 7.7% on bioconductor.org
3 versions - Latest release: 6 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: 6 months ago - 37.4 thousand downloads total - 1 maintainer
ISoLDE 1.30.0
Integrative Statistics of alleLe Dependent Expression3 versions - Latest release: 6 months ago - 9.18 thousand downloads total - 1 maintainer
cydar 1.26.0
Using Mass Cytometry for Differential Abundance Analyses3 versions - Latest release: 6 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: 6 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: 6 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: 13 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: 13 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: 6 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: 6 months ago - 34.8 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 7.6% on bioconductor.org
3 versions - Latest release: 6 months ago - 32.6 thousand downloads total - 1 maintainer
Mulcom 1.52.0
Calculates Mulcom test3 versions - Latest release: 6 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: 6 months ago - 4.84 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
TTMap 1.24.0
Two-Tier Mapper: a clustering tool based on topological data analysis3 versions - Latest release: 6 months ago - 6.96 thousand downloads total - 1 maintainer
omicade4 1.42.0
Multiple co-inertia analysis of omics datasets3 versions - Latest release: 6 months ago - 5 dependent packages - 24.7 thousand downloads total - 1 maintainer
Top 7.9% on bioconductor.org
3 versions - Latest release: 6 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: 6 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: 20 days 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: 6 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: 6 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: 6 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: 6 months ago - 4.2 thousand downloads total - 8 stars on GitHub - 1 maintainer
qsmooth 1.18.0
Smooth quantile normalization3 versions - Latest release: 6 months ago - 7.31 thousand downloads total - 1 maintainer
Top 7.6% on bioconductor.org
3 versions - Latest release: 6 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: 6 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: 6 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: 6 months ago - 9.28 thousand downloads total - 1 maintainer
snm 1.50.0
Supervised Normalization of Microarrays3 versions - Latest release: 6 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: 6 months ago - 11.8 thousand downloads total - 1 maintainer
R4RNA 1.30.0
An R package for RNA visualization and analysis3 versions - Latest release: 6 months ago - 2 dependent packages - 30 thousand downloads total - 1 maintainer
openPrimeR 1.24.0
Multiplex PCR Primer Design and Analysis3 versions - Latest release: 6 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: 6 months ago - 3.5 thousand downloads total - 1 maintainer
edge 2.34.0
Extraction of Differential Gene Expression3 versions - Latest release: 6 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: 6 months ago - 1 dependent package - 22 thousand downloads total - 1 maintainer
Top 8.4% on bioconductor.org
3 versions - Latest release: 6 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: 6 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: 6 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: 6 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: 6 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: 6 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: 6 months ago - 8.96 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 7.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 38.4 thousand downloads total - 1 maintainer
GeneOverlap 1.38.0
Test and visualize gene overlaps3 versions - Latest release: 6 months ago - 1 dependent package - 38.4 thousand downloads total - 1 maintainer
Top 6.5% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 38.4 thousand downloads total - 1 maintainer
parody 1.60.0
Parametric And Resistant Outlier DYtection3 versions - Latest release: 6 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: 6 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: 6 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: 6 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: 6 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: 6 months ago - 20.3 thousand downloads total - 1 maintainer
Top 7.3% on bioconductor.org
3 versions - Latest release: 6 months ago - 32.8 thousand downloads total - 1 maintainer
RBioinf 1.62.0
RBioinf3 versions - Latest release: 6 months ago - 32.8 thousand downloads total - 1 maintainer
regioneReloaded 1.4.0
RegioneReloaded: Multiple Association for Genomic Region Sets3 versions - Latest release: 6 months ago - 1.61 thousand downloads total - 5 stars on GitHub - 1 maintainer
PloGO2 1.14.0
Plot Gene Ontology and KEGG pathway Annotation and Abundance3 versions - Latest release: 6 months ago - 4.63 thousand downloads total - 2 maintainers
dks 1.48.0
The double Kolmogorov-Smirnov package for evaluating multiple testing procedures.3 versions - Latest release: 6 months ago - 21.6 thousand downloads total - 1 maintainer
normr 1.28.0
Normalization and difference calling in ChIP-seq data3 versions - Latest release: 6 months ago - 15.7 thousand downloads total - 11 stars on GitHub - 1 maintainer
globalSeq 1.30.0
Global Test for Counts3 versions - Latest release: 6 months ago - 10.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
MBttest 1.30.0
Multiple Beta t-Tests3 versions - Latest release: 6 months ago - 9.63 thousand downloads total - 1 maintainer
ssviz 1.36.0
A small RNA-seq visualizer and analysis toolkit2 versions - Latest release: 6 months ago - 14.8 thousand downloads total - 1 maintainer
BGmix 1.62.0 removed
Bayesian models for differential gene expression2 versions - Latest release: 6 months ago - 22 thousand downloads total - 1 maintainer
TVTB 1.28.0
TVTB: The VCF Tool Box3 versions - Latest release: 6 months ago - 9.85 thousand downloads total - 2 stars on GitHub - 1 maintainer
clippda 1.52.0
A package for the clinical proteomic profiling data analysis3 versions - Latest release: 6 months ago - 27.7 thousand downloads total - 1 maintainer
ViSEAGO 1.16.0
ViSEAGO: a Bioconductor package for clustering biological functions using Gene Ontology and seman...3 versions - Latest release: 6 months ago - 12 thousand downloads total - 1 maintainer
MultiMed 2.24.0
Testing multiple biological mediators simultaneously3 versions - Latest release: 6 months ago - 13.6 thousand downloads total - 1 maintainer
ChIPComp 1.32.0
Quantitative comparison of multiple ChIP-seq datasets3 versions - Latest release: 6 months ago - 14.4 thousand downloads total - 1 maintainer
mCSEA 1.22.0
Methylated CpGs Set Enrichment Analysis3 versions - Latest release: 6 months ago - 1 dependent package - 9.56 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
4 versions - Latest release: 4 months ago - 1 dependent package - 28 thousand downloads total - 1 maintainer
EGSEA 1.30.1
Ensemble of Gene Set Enrichment Analyses4 versions - Latest release: 4 months ago - 1 dependent package - 28 thousand downloads total - 1 maintainer
consensusDE 1.20.0
RNA-seq analysis using multiple algorithms3 versions - Latest release: 6 months ago - 7.42 thousand downloads total - 1 maintainer
deco 1.18.0 removed
Decomposing Heterogeneous Cohorts using Omic Data Profiling2 versions - Latest release: 6 months ago - 4.59 thousand downloads total - 4 stars on GitHub - 1 maintainer
CellScore 1.22.0
Tool for Evaluation of Cell Identity from Transcription Profiles3 versions - Latest release: 6 months ago - 7.15 thousand downloads total - 1 maintainer
Top 7.8% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 31.5 thousand downloads total - 1 maintainer
phenoTest 1.50.0
Tools to test association between gene expression and phenotype in a way that is efficient, struc...3 versions - Latest release: 6 months ago - 1 dependent package - 31.5 thousand downloads total - 1 maintainer
gCrisprTools 2.8.0
Suite of Functions for Pooled Crispr Screen QC and Analysis3 versions - Latest release: 6 months ago - 11.6 thousand downloads total - 1 maintainer
PROMISE 1.54.0
PRojection Onto the Most Interesting Statistical Evidence3 versions - Latest release: 6 months ago - 1 dependent package - 24.9 thousand downloads total - 2 maintainers
consensusSeekeR 1.30.0
Detection of consensus regions inside a group of experiences using genomic positions and genomic ...3 versions - Latest release: 6 months ago - 2 dependent packages - 12.7 thousand downloads total - 1 stars on GitHub - 1 maintainer
metaseqR2 1.14.0
An R package for the analysis and result reporting of RNA-Seq data by combining multiple statisti...3 versions - Latest release: 6 months ago - 5.12 thousand downloads total - 1 maintainer
sights 1.28.0
Statistics and dIagnostic Graphs for HTS3 versions - Latest release: 6 months ago - 9.64 thousand downloads total - 0 stars on GitHub - 1 maintainer
Sconify 1.22.0
A toolkit for performing KNN-based statistics for flow and mass cytometry data3 versions - Latest release: 6 months ago - 7.2 thousand downloads total - 1 maintainer
omicRexposome 1.24.3
Exposome and omic data associatin and integration analysis4 versions - Latest release: 3 months ago - 7.99 thousand downloads total - 1 maintainer
Top 8.4% on bioconductor.org
3 versions - Latest release: 6 months ago - 31.9 thousand downloads total - 1 maintainer
fdrame 1.74.0
FDR adjustments of Microarray Experiments (FDR-AME)3 versions - Latest release: 6 months ago - 31.9 thousand downloads total - 1 maintainer
matchBox 1.44.0
Utilities to compute, compare, and plot the agreement between ordered vectors of features (ie. di...3 versions - Latest release: 6 months ago - 19.4 thousand downloads total - 2 maintainers
unifiedWMWqPCR 1.38.0
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data3 versions - Latest release: 6 months ago - 15.5 thousand downloads total - 1 maintainer
meshes 1.28.0
MeSH Enrichment and Semantic analyses3 versions - Latest release: 6 months ago - 16.4 thousand downloads total - 1 maintainer
microSTASIS 1.2.0
Microbiota STability ASsessment via Iterative cluStering3 versions - Latest release: 6 months ago - 1.44 thousand downloads total - 1 maintainer
semisup 1.26.0
Semi-Supervised Mixture Model3 versions - Latest release: 6 months ago - 7.99 thousand downloads total - 1 stars on GitHub - 1 maintainer
scShapes 1.8.0
A Statistical Framework for Modeling and Identifying Differential Distributions in Single-cell RN...3 versions - Latest release: 6 months ago - 2.18 thousand downloads total - 7 stars on GitHub - 1 maintainer
CoSIA 1.2.0
An Investigation Across Different Species and Tissues3 versions - Latest release: 6 months ago - 1.05 thousand downloads total - 1 maintainer
seqsetvis 1.22.1
Set Based Visualizations for Next-Gen Sequencing Data4 versions - Latest release: 2 months ago - 8.78 thousand downloads total - 1 maintainer
rain 1.36.0
Rhythmicity Analysis Incorporating Non-parametric Methods3 versions - Latest release: 6 months ago - 19.2 thousand downloads total - 1 maintainer
phemd 1.18.0
Phenotypic EMD for comparison of single-cell samples3 versions - Latest release: 6 months ago - 5.54 thousand downloads total - 1 maintainer
staRank 1.44.0
Stability Ranking3 versions - Latest release: 6 months ago - 19.6 thousand downloads total - 1 maintainer
EBSeqHMM 1.35.0
Bayesian analysis for identifying gene or isoform expression changes in ordered RNA-seq experiments3 versions - Latest release: 6 months ago - 17.4 thousand downloads total - 1 maintainer
GOpro 1.28.0
Find the most characteristic gene ontology terms for groups of human genes3 versions - Latest release: 6 months ago - 15 thousand downloads total - 2 stars on GitHub - 1 maintainer
GEWIST 1.46.0
Gene Environment Wide Interaction Search Threshold3 versions - Latest release: 6 months ago - 20.1 thousand downloads total - 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
DataImport
25
GeneSetEnrichment
25
Classification
24
QualityControl
24
StatisticalMethod
23
Transcriptomics
22
Annotation
21
Bayesian
20
SingleCell
20
Proteomics
20
ChIPSeq
18
BatchEffect
18
Pathways
18
FunctionalGenomics
16
BiomedicalInformatics
16
Epigenetics
16
TimeCourse
16
Coverage
15
GO
14
SystemsBiology
14
DifferentialSplicing
13
AlternativeSplicing
13
Alignment
13
SNP
12
bioconductor
12
OneChannel
12
DataRepresentation
11
TwoChannel
10
Metabolomics
10
r
10
DNAMethylation
9
GeneticVariability
9
CellBiology
9
Metagenomics
9
DifferentialMethylation
9
Microbiome
9
GUI
9
DifferentialPeakCalling
8
GeneTarget
8
mRNAMicroarray
8
PrincipalComponent
7
KEGG
7
DimensionReduction
7
GenomeWideAssociation
7
FeatureExtraction
7
ExonArray
7
ReportWriting
6
GeneRegulation
6
FlowCytometry
6
ATACSeq
6
GenomeAnnotation
5
bioconductor-package
5
ProprietaryPlatforms
5
Network
5
WholeGenome
5
Reactome
5
BiologicalQuestion
5
ExperimentalDesign
5
MassSpectrometry
5
GenomicVariation
5
GenePrediction
5
GraphAndNetwork
5
DNASeq
5
MethylationArray
5
MicrotitrePlateAssay
4
CopyNumberVariation
4
WorkflowStep
4
MicroRNAArray
4
bioinformatics
4
PeakDetection
4
MethylSeq
4
Survival
4
gene-expression
3
HiddenMarkovModel
3
shiny
3
FunctionalPrediction
3
Technology
3
Infrastructure
3
HistoneModification
3
SequenceMatching
3
SAGE
3
MultipleSequenceAlignment
3
epigenomics
2
NetworkEnrichment
2
DNaseSeq
2
RIPSeq
2