Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "KEGG" keyword
UniProt.ws 2.44.0
R Interface to UniProt Web Services3 versions - Latest release: about 1 month ago - 6 dependent packages - 54.8 thousand downloads total - 4 stars on GitHub - 1 maintainer
ginmappeR 1.0.0
Gene Identifier Mapper1 version - Latest release: about 1 month ago - 323 downloads total - 1 maintainer
Top 1.9% on bioconductor.org
3 versions - Latest release: about 1 month ago - 15 dependent packages - 1.19 million downloads total - 1 maintainer
enrichplot 1.24.0
Visualization of Functional Enrichment Result3 versions - Latest release: about 1 month ago - 15 dependent packages - 1.19 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
4 versions - Latest release: about 1 month 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: about 1 month ago - 59 dependent packages - 1.41 million downloads total - 1 maintainer
Top 1.2% on bioconductor.org
3 versions - Latest release: about 1 month ago - 35 dependent packages - 2.43 million downloads total - 1 maintainer
KEGGREST 1.44.0
Client-side REST access to the Kyoto Encyclopedia of Genes and Genomes (KEGG)3 versions - Latest release: about 1 month ago - 35 dependent packages - 2.43 million downloads total - 1 maintainer
Top 1.4% on bioconductor.org
3 versions - Latest release: about 1 month ago - 49 dependent packages - 983 thousand downloads total - 1 maintainer
GSEABase 1.66.0
Gene set enrichment data structures and methods3 versions - Latest release: about 1 month ago - 49 dependent packages - 983 thousand downloads total - 1 maintainer
cogena 1.36.0
co-expressed gene-set enrichment analysis3 versions - Latest release: 7 months ago - 17.9 thousand downloads total - 12 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 11 dependent packages - 233 thousand downloads total - 5 stars on GitHub - 1 maintainer
graphite 1.48.0
GRAPH Interaction from pathway Topological Environment3 versions - Latest release: 6 months ago - 11 dependent packages - 233 thousand downloads total - 5 stars on GitHub - 1 maintainer
mirIntegrator 1.32.0
Integrating microRNA expression into signaling pathways for pathway analysis3 versions - Latest release: 6 months ago - 12.1 thousand downloads total - 1 stars on GitHub - 1 maintainer
famat 1.12.0
Functional analysis of metabolic and transcriptomic data3 versions - Latest release: 6 months ago - 3.63 thousand downloads total - 1 stars on GitHub - 1 maintainer
fenr 1.0.5
Fast functional enrichment for interactive applications5 versions - Latest release: 3 months ago - 1.09 thousand downloads total - 0 stars on GitHub - 1 maintainer
RegionalST 1.0.1
Investigating regions of interest and performing cross-regional analysis with spatial transcripto...3 versions - Latest release: 5 months ago - 1.07 thousand downloads total - 1 maintainer
RandomWalkRestartMH 1.22.0
Random walk with restart on multiplex and heterogeneous Networks3 versions - Latest release: 6 months ago - 1 dependent package - 9.5 thousand downloads total - 17 stars on GitHub - 1 maintainer
Top 2.7% on bioconductor.org
3 versions - Latest release: 7 months ago - 13 dependent packages - 541 thousand downloads total - 1 maintainer
KEGGgraph 1.62.0
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor3 versions - Latest release: 7 months ago - 13 dependent packages - 541 thousand downloads total - 1 maintainer
paxtoolsr 1.36.0
Access Pathways from Multiple Databases Through BioPAX and Pathway Commons3 versions - Latest release: 6 months ago - 24 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 7.7% on bioconductor.org
3 versions - Latest release: 7 months ago - 36.3 thousand downloads total - 2 maintainers
GDCRNATools 1.22.0
GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, mRNA, and miRNA data i...3 versions - Latest release: 7 months ago - 36.3 thousand downloads total - 2 maintainers
OmnipathR 3.10.1
OmniPath web service client and more3 versions - Latest release: 7 months ago - 3 dependent packages - 23.4 thousand downloads total - 1 maintainer
PanViz 1.4.0
Integrating Multi-Omic Network Data With Summay-Level GWAS Data3 versions - Latest release: 7 months ago - 1.66 thousand downloads total - 3 stars on GitHub - 1 maintainer
dce 1.10.0
Pathway Enrichment Based on Differential Causal Effects3 versions - Latest release: 7 months ago - 3.73 thousand downloads total - 9 stars on GitHub - 1 maintainer
CTDquerier 2.10.0
Package for CTDbase data query, visualization and downstream analysis3 versions - Latest release: 7 months ago - 5.56 thousand downloads total - 1 maintainer
phenomis 1.4.0
Postprocessing and univariate analysis of omics data3 versions - Latest release: 7 months ago - 1.98 thousand downloads total - 1 maintainer
Top 9.3% on bioconductor.org
3 versions - Latest release: 7 months ago - 1 dependent package - 32.7 thousand downloads total - 1 maintainer
MAGeCKFlute 2.6.0
Integrative Analysis Pipeline for Pooled CRISPR Functional Genetic Screens3 versions - Latest release: 7 months ago - 1 dependent package - 32.7 thousand downloads total - 1 maintainer
slalom 1.24.0
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data3 versions - Latest release: 7 months ago - 9.37 thousand downloads total - 1 maintainer
ADAMgui 1.18.0
Activity and Diversity Analysis Module Graphical User Interface3 versions - Latest release: 7 months ago - 6.89 thousand downloads total - 1 maintainer
BPRMeth 1.28.0
Model higher-order methylation profiles3 versions - Latest release: 7 months ago - 1 dependent package - 11.9 thousand downloads total - 1 maintainer
Top 7.8% on bioconductor.org
3 versions - Latest release: 7 months ago - 1 dependent package - 39 thousand downloads total - 1 maintainer
keggorthology 2.54.0
graph support for KO, KEGG Orthology3 versions - Latest release: 7 months ago - 1 dependent package - 39 thousand downloads total - 1 maintainer
MetaPhOR 1.4.0
Metabolic Pathway Analysis of RNA3 versions - Latest release: 7 months ago - 1.67 thousand downloads total - 1 maintainer
DEsubs 1.28.0
DEsubs: an R package for flexible identification of differentially expressed subpathways using RN...3 versions - Latest release: 7 months ago - 11.1 thousand downloads total - 2 maintainers
coRdon 1.20.0
Codon Usage Analysis and Prediction of Gene Expressivity3 versions - Latest release: 7 months ago - 13 thousand downloads total - 17 stars on GitHub - 1 maintainer
scBFA 1.16.0
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile...3 versions - Latest release: 7 months ago - 5.39 thousand downloads total - 1 maintainer
Top 9.0% on bioconductor.org
3 versions - Latest release: 7 months ago - 2 dependent packages - 29.4 thousand downloads total - 1 maintainer
MLP 1.50.0
Mean Log P Analysis3 versions - Latest release: 7 months ago - 2 dependent packages - 29.4 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
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
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
GRridge 1.26.0 removed
Better prediction by use of co-data: Adaptive group-regularized ridge regression2 versions - Latest release: 7 months ago - 7.94 thousand downloads total - 1 maintainer
PloGO2 1.14.0
Plot Gene Ontology and KEGG pathway Annotation and Abundance3 versions - Latest release: 7 months ago - 4.63 thousand downloads total - 2 maintainers
transomics2cytoscape 1.12.0
A tool set for 3D Trans-Omic network visualization with Cytoscape3 versions - Latest release: 7 months ago - 3.65 thousand downloads total - 1 maintainer
Melissa 1.18.0
Bayesian clustering and imputationa of single cell methylomes3 versions - Latest release: 7 months ago - 5.54 thousand downloads total - 1 maintainer
attract 1.54.0
Methods to Find the Gene Expression Modules that Represent the Drivers of Kauffman's Attractor La...3 versions - Latest release: 7 months ago - 29.9 thousand downloads total - 1 maintainer
VaSP 1.14.0
Quantification and Visualization of Variations of Splicing in Population3 versions - Latest release: 7 months ago - 3.14 thousand downloads total - 3 stars on GitHub - 1 maintainer
BiocSet 1.16.1
Representing Different Biological Sets3 versions - Latest release: 3 months ago - 4 dependent packages - 15.2 thousand downloads total - 1 maintainer
MetaboSignal 1.32.1
MetaboSignal: a network-based approach to overlay and explore metabolic and signaling KEGG pathways3 versions - Latest release: 6 months ago - 13.6 thousand downloads total - 2 maintainers
MetID 1.20.0
Network-based prioritization of putative metabolite IDs3 versions - Latest release: 7 months ago - 5.66 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 9.8% on bioconductor.org
4 versions - Latest release: 5 months ago - 1 dependent package - 28 thousand downloads total - 1 maintainer
EGSEA 1.30.1
Ensemble of Gene Set Enrichment Analyses4 versions - Latest release: 5 months ago - 1 dependent package - 28 thousand downloads total - 1 maintainer
StarBioTrek 1.28.0
StarBioTrek3 versions - Latest release: 7 months ago - 10 thousand downloads total - 0 stars on GitHub - 1 maintainer
ADAM 1.18.0
ADAM: Activity and Diversity Analysis Module3 versions - Latest release: 7 months ago - 1 dependent package - 7.52 thousand downloads total - 1 maintainer
signatureSearch 1.16.0
Environment for Gene Expression Searching Combined with Functional Enrichment Analysis3 versions - Latest release: 7 months ago - 10.6 thousand downloads total - 17 stars on GitHub - 1 maintainer
dearseq 1.14.0
Differential Expression Analysis for RNA-seq data through a robust variance component test3 versions - Latest release: 7 months ago - 2 dependent packages - 8.25 thousand downloads total - 6 stars on GitHub - 1 maintainer
CHRONOS 1.30.0
CHRONOS: A time-varying method for microRNA-mediated sub-pathway enrichment analysis3 versions - Latest release: 7 months ago - 12 thousand downloads total - 1 maintainer
pairkat 1.8.0
PaIRKAT3 versions - Latest release: 7 months ago - 2.16 thousand downloads total - 0 stars on GitHub - 1 maintainer
biodb 1.10.0
biodb, a library and a development framework for connecting to chemical and biological databases3 versions - Latest release: 7 months ago - 10 dependent packages - 7.13 thousand downloads total - 11 stars on GitHub - 1 maintainer
biodbKegg 1.8.0
biodbKegg, a library for connecting to the KEGG Database3 versions - Latest release: 7 months ago - 2.86 thousand downloads total - 2 stars on GitHub - 1 maintainer
KEGGlincs 1.28.0
Visualize all edges within a KEGG pathway and overlay LINCS data3 versions - Latest release: 7 months ago - 10.9 thousand downloads total - 2 maintainers
FELLA 1.22.0
Interpretation and enrichment for metabolomics data3 versions - Latest release: 7 months ago - 13.6 thousand downloads total - 1 maintainer
GeDi 1.0.0
Defining and visualizing the distances between different genesets1 version - Latest release: about 1 month ago - 148 downloads total - 1 stars on GitHub - 1 maintainer
ggkegg 1.0.13
KEGG pathway visualization by ggplot28 versions - Latest release: 3 months ago - 3.39 thousand downloads total - 191 stars on GitHub - 1 maintainer
MicrobiomeProfiler 1.10.0
An R/shiny package for microbiome functional enrichment analysis3 versions - Latest release: 19 days ago - 3.56 thousand downloads total - 33 stars on GitHub - 1 maintainer
InterMineR 1.26.0
R Interface with InterMine-Powered Databases4 versions - Latest release: 24 days ago - 10.4 thousand downloads total - 17 stars on GitHub - 1 maintainer
iNETgrate 1.2.0
Integrates DNA methylation data with gene expression in a single gene network2 versions - Latest release: 25 days ago - 970 downloads total - 65 stars on GitHub - 1 maintainer
MIGSA 1.24.0 removed
Massive and Integrative Gene Set Analysis1 version - Latest release: 8 months ago - 7.89 thousand downloads total - 0 stars on GitHub - 1 maintainer
ASpediaFI 1.14.0 removed
ASpedia-FI: Functional Interaction Analysis of Alternative Splicing Events1 version - Latest release: 8 months ago - 3.82 thousand downloads total - 1 stars on GitHub - 1 maintainer
netboxr 1.11.0 removed
netboxr1 version - Latest release: 8 months ago - 2.92 thousand downloads total - 1 maintainer
Related Keywords
Software
62
Pathways
39
GeneExpression
26
GeneSetEnrichment
25
Network
22
GraphAndNetwork
22
GO
20
Reactome
17
Visualization
16
RNASeq
14
DifferentialExpression
11
SystemsBiology
11
ImmunoOncology
11
Clustering
11
NetworkEnrichment
10
Sequencing
10
Annotation
9
Microarray
9
Transcriptomics
7
Metabolomics
7
r
7
DataImport
7
MultipleComparison
7
Regression
6
GeneRegulation
6
Genetics
6
NetworkInference
5
Coverage
5
BiomedicalInformatics
5
SingleCell
5
Normalization
5
ThirdPartyClient
5
Infrastructure
5
GeneTarget
4
DataRepresentation
4
StatisticalMethod
4
Proteomics
4
GenePrediction
4
Survival
3
DNAMethylation
3
bioinformatics
3
Bayesian
3
DimensionReduction
3
Transcription
3
GeneSignaling
3
QualityControl
3
Classification
3
AlternativeSplicing
3
FunctionalPrediction
3
biology
2
FeatureExtraction
2
Epigenetics
2
GenomeWideAssociation
2
SNP
2
kegg
2
BatchEffect
2
FunctionalGenomics
2
GUI
2
BioCarta
2
CellBiology
2
bioconductor
2
pathways
2
visualization
2
CRISPR
1
rna-seq
1
splicing
1
sqtl
1
statistics
1
AssayDomain
1
BiologicalQuestion
1
TimeCourse
1
ResearchField
1
Technology
1
WorkflowStep
1
OneChannel
1
TwoChannel
1
DNASeq
1
r-package
1
cran
1
core-services
1
mRNAMicroarray
1
PrincipalComponent
1
intermine
1
genomics
1
GenomeAnnotation
1
ComparativeGenomics
1
Microbiome
1
tidygraph
1
pathway
1
ggraph
1
ggplot2
1
ShinyApps
1
ReportWriting
1
kegg-databases
1
biodb
1
databases
1
chemistry
1
cheminformatics
1
MassSpectrometry
1
causality
1