Ecosyste.ms: Packages
An open API service providing package, version and dependency metadata of many open source software ecosystems and registries.
bioconductor.org "Clustering" keyword
DrugVsDisease 2.44.0
Comparison of disease and drug profiles using Gene set Enrichment Analysis3 versions - Latest release: 6 months ago - 22.1 thousand downloads total - 1 maintainer
vsclust 1.4.0
Feature-based variance-sensitive quantitative clustering3 versions - Latest release: 6 months ago - 1.7 thousand downloads total - 1 maintainer
microbiomeExplorer 1.12.0
Microbiome Exploration App3 versions - Latest release: 6 months ago - 6.29 thousand downloads total - 1 maintainer
Top 4.4% on bioconductor.org
4 versions - Latest release: 5 days ago - 5 dependent packages - 197 thousand downloads total - 162 stars on GitHub - 1 maintainer
SingleR 2.6.0
Reference-Based Single-Cell RNA-Seq Annotation4 versions - Latest release: 5 days ago - 5 dependent packages - 197 thousand downloads total - 162 stars on GitHub - 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
CelliD 1.10.1
Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis4 versions - Latest release: 5 months ago - 9.32 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
Top 7.5% on bioconductor.org
3 versions - Latest release: 6 months ago - 41.6 thousand downloads total - 1 maintainer
BHC 1.54.0
Bayesian Hierarchical Clustering3 versions - Latest release: 6 months ago - 41.6 thousand downloads total - 1 maintainer
FEAST 1.10.0
FEAture SelcTion (FEAST) for Single-cell clustering3 versions - Latest release: 6 months ago - 4.7 thousand downloads total - 9 stars on GitHub - 1 maintainer
FunChIP 1.28.0
Clustering and Alignment of ChIP-Seq peaks based on their shapes3 versions - Latest release: 6 months ago - 9.68 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
Top 6.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 42 thousand downloads total - 1 maintainer
clusterStab 1.74.0
Compute cluster stability scores for microarray data3 versions - Latest release: 6 months ago - 42 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
Top 8.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 30.1 thousand downloads total - 1 maintainer
maigesPack 1.66.0
Functions to handle cDNA microarray data, including several methods of data analysis3 versions - Latest release: 6 months ago - 30.1 thousand downloads total - 1 maintainer
Linnorm 2.26.0
Linear model and normality based normalization and transformation method (Linnorm)3 versions - Latest release: 6 months ago - 1 dependent package - 22.4 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
CuratedAtlasQueryR 1.2.0
Queries the Human Cell Atlas3 versions - Latest release: 15 days ago - 1.07 thousand downloads total - 77 stars on GitHub - 1 maintainer
phantasus 1.22.2
Visual and interactive gene expression analysis3 versions - Latest release: 6 months ago - 11 thousand downloads total - 1 maintainer
SpacePAC 1.40.0
Identification of Mutational Clusters in 3D Protein Space via Simulation.3 versions - Latest release: 6 months ago - 1 dependent package - 18.2 thousand downloads total - 1 maintainer
netboost 2.10.0
Network Analysis Supported by Boosting3 versions - Latest release: 6 months ago - 4.72 thousand downloads total - 1 maintainer
powerTCR 1.22.0
Model-Based Comparative Analysis of the TCR Repertoire3 versions - Latest release: 6 months ago - 1 dependent package - 26.9 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
IRISFGM 1.10.0
Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq3 versions - Latest release: 6 months ago - 3 thousand downloads total - 1 maintainer
concordexR 1.2.0
Calculate the concordex coefficient3 versions - Latest release: 6 months ago - 1.67 thousand downloads total - 6 stars on GitHub - 1 maintainer
rScudo 1.18.1
Signature-based Clustering for Diagnostic Purposes4 versions - Latest release: 3 months ago - 5.75 thousand downloads total - 3 stars on GitHub - 1 maintainer
SigFuge 1.40.0
SigFuge3 versions - Latest release: 6 months ago - 17.1 thousand downloads total - 1 maintainer
stJoincount 1.4.0
stJoincount - Join count statistic for quantifying spatial correlation between clusters3 versions - Latest release: 6 months ago - 1.81 thousand downloads total - 5 stars on GitHub - 1 maintainer
BOBaFIT 1.6.0
Refitting diploid region profiles using a clustering procedure3 versions - Latest release: 6 months ago - 2.28 thousand downloads total - 0 stars on GitHub - 1 maintainer
GARS 1.22.0
GARS: Genetic Algorithm for the identification of Robust Subsets of variables in high-dimensional...3 versions - Latest release: 6 months ago - 8.17 thousand downloads total - 1 maintainer
consensusOV 1.24.0
Gene expression-based subtype classification for high-grade serous ovarian cancer3 versions - Latest release: 6 months ago - 1 dependent package - 9.83 thousand downloads total - 1 maintainer
CancerSubtypes 1.28.0
Cancer subtypes identification, validation and visualization based on multiple genomic data sets3 versions - Latest release: 6 months ago - 21.1 thousand downloads total - 13 stars on GitHub - 1 maintainer
ccImpute 1.4.0
ccImpute: an accurate and scalable consensus clustering based approach to impute dropout events i...3 versions - Latest release: 6 months ago - 1.65 thousand downloads total - 1 stars on GitHub - 1 maintainer
clustComp 1.30.0
Clustering Comparison Package3 versions - Latest release: 6 months ago - 11 thousand downloads total - 1 maintainer
ppcseq 1.10.0
Probabilistic Outlier Identification for RNA Sequencing Generalized Linear Models3 versions - Latest release: 6 months ago - 2.85 thousand downloads total - 6 stars on GitHub - 1 maintainer
omada 1.4.0
Machine learning tools for automated transcriptome clustering analysis3 versions - Latest release: 6 months ago - 1.5 thousand downloads total - 1 maintainer
Top 9.5% on bioconductor.org
3 versions - Latest release: 6 months ago - 29.4 thousand downloads total - 1 maintainer
GOSim 1.40.0
Computation of functional similarities between GO terms and gene products; GO enrichment analysis3 versions - Latest release: 6 months ago - 29.4 thousand downloads total - 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
SynExtend 1.14.0
Tools for Working With Synteny Objects3 versions - Latest release: 6 months ago - 4.41 thousand downloads total - 1 maintainer
hierinf 1.20.0
Hierarchical Inference3 versions - Latest release: 6 months ago - 5.33 thousand downloads total - 1 maintainer
phenomis 1.4.0
Postprocessing and univariate analysis of omics data3 versions - Latest release: 6 months ago - 1.98 thousand downloads total - 1 maintainer
GmicR 1.16.0
Combines WGCNA and xCell readouts with bayesian network learrning to generate a Gene-Module Immun...3 versions - Latest release: 6 months ago - 5.69 thousand downloads total - 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
ddPCRclust 1.22.0
Clustering algorithm for ddPCR data3 versions - Latest release: 6 months ago - 7.69 thousand downloads total - 4 stars on GitHub - 1 maintainer
STATegRa 1.38.0
Classes and methods for multi-omics data integration3 versions - Latest release: 6 months ago - 15.5 thousand downloads total - 2 maintainers
PING 2.46.0
Probabilistic inference for Nucleosome Positioning with MNase-based or Sonicated Short-read Data3 versions - Latest release: 6 months ago - 23.7 thousand downloads total - 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
deltaGseg 1.42.0
deltaGseg3 versions - Latest release: 6 months ago - 19.2 thousand downloads total - 1 maintainer
Macarron 1.6.0
Prioritization of potentially bioactive metabolic features from epidemiological and environmental...3 versions - Latest release: 6 months ago - 1.93 thousand downloads total - 1 maintainer
treekoR 1.10.0
Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations3 versions - Latest release: 6 months ago - 2.99 thousand downloads total - 1 maintainer
fcScan 1.16.0
fcScan for detecting clusters of coordinates with user defined options3 versions - Latest release: 6 months ago - 5.68 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
ANF 1.24.1
Affinity Network Fusion for Complex Patient Clustering4 versions - Latest release: 3 months ago - 8.71 thousand downloads total - 1 maintainer
hierGWAS 1.32.0
Asessing statistical significance in predictive GWA studies3 versions - Latest release: 6 months ago - 11.7 thousand downloads total - 1 maintainer
Top 6.1% on bioconductor.org
3 versions - Latest release: 6 months ago - 4 dependent packages - 53.1 thousand downloads total - 36 stars on GitHub - 1 maintainer
clusterExperiment 2.22.0
Compare Clusterings for Single-Cell Sequencing3 versions - Latest release: 6 months ago - 4 dependent packages - 53.1 thousand downloads total - 36 stars on GitHub - 1 maintainer
Spaniel 1.16.0
Spatial Transcriptomics Analysis3 versions - Latest release: 6 months ago - 6.46 thousand downloads total - 1 maintainer
mosbi 1.8.0
Molecular Signature identification using Biclustering3 versions - Latest release: 6 months ago - 2.63 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
Top 9.6% on bioconductor.org
3 versions - Latest release: 6 months ago - 28.8 thousand downloads total - 1 maintainer
CORREP 1.68.0
Multivariate Correlation Estimator and Statistical Inference Procedures.3 versions - Latest release: 6 months ago - 28.8 thousand downloads total - 1 maintainer
BPRMeth 1.28.0
Model higher-order methylation profiles3 versions - Latest release: 6 months ago - 1 dependent package - 11.9 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
flowMeans 1.62.0
Non-parametric Flow Cytometry Data Gating3 versions - Latest release: 6 months ago - 2 dependent packages - 45.4 thousand downloads total - 1 maintainer
HGC 1.10.0
A fast hierarchical graph-based clustering method3 versions - Latest release: 6 months ago - 3.61 thousand downloads total - 1 maintainer
Top 9.8% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 26.8 thousand downloads total - 1 maintainer
FGNet 3.36.0
Functional Gene Networks derived from biological enrichment analyses3 versions - Latest release: 6 months ago - 1 dependent package - 26.8 thousand downloads total - 1 maintainer
scMET 1.4.0
Bayesian modelling of cell-to-cell DNA methylation heterogeneity3 versions - Latest release: 6 months ago - 1.73 thousand downloads total - 18 stars on GitHub - 1 maintainer
SANTA 2.38.0
Spatial Analysis of Network Associations3 versions - Latest release: 6 months ago - 18.7 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 6.2% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 48.8 thousand downloads total - 2 maintainers
iClusterPlus 1.38.0
Integrative clustering of multi-type genomic data3 versions - Latest release: 6 months ago - 1 dependent package - 48.8 thousand downloads total - 2 maintainers
immunoClust 1.34.0
immunoClust - Automated Pipeline for Population Detection in Flow Cytometry3 versions - Latest release: 6 months ago - 13.4 thousand downloads total - 1 maintainer
CellTrails 1.20.0
Reconstruction, visualization and analysis of branching trajectories3 versions - Latest release: 6 months ago - 6.81 thousand downloads total - 1 maintainer
ccfindR 1.22.0
Cancer Clone Finder3 versions - Latest release: 6 months ago - 1 dependent package - 11.4 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 8.9% on bioconductor.org
3 versions - Latest release: 6 months ago - 2 dependent packages - 32.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
kebabs 1.36.0
Kernel-Based Analysis of Biological Sequences3 versions - Latest release: 6 months ago - 2 dependent packages - 32.9 thousand downloads total - 0 stars on GitHub - 1 maintainer
Pigengene 1.28.0
Infers biological signatures from gene expression data3 versions - Latest release: 6 months ago - 1 dependent package - 13.6 thousand downloads total - 1 maintainer
Top 7.7% on bioconductor.org
3 versions - Latest release: 6 months ago - 3 dependent packages - 65.1 thousand downloads total - 1 maintainer
supraHex 1.40.0
supraHex: a supra-hexagonal map for analysing tabular omics data3 versions - Latest release: 6 months ago - 3 dependent packages - 65.1 thousand downloads total - 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
SCFA 1.12.0
SCFA: Subtyping via Consensus Factor Analysis3 versions - Latest release: 6 months ago - 3.45 thousand downloads total - 3 stars on GitHub - 1 maintainer
cytoKernel 1.8.0
Differential expression using kernel-based score test3 versions - Latest release: 6 months ago - 2.32 thousand downloads total - 0 stars on GitHub - 1 maintainer
Top 7.3% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 36.6 thousand downloads total - 1 maintainer
flowMerge 2.50.0
Cluster Merging for Flow Cytometry Data3 versions - Latest release: 6 months ago - 1 dependent package - 36.6 thousand downloads total - 1 maintainer
FuseSOM 1.4.0
A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets3 versions - Latest release: 6 months ago - 1.79 thousand downloads total - 1 stars on GitHub - 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
flowMatch 1.38.0
Matching and meta-clustering in flow cytometry3 versions - Latest release: 6 months ago - 17.5 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
Top 7.9% on bioconductor.org
3 versions - Latest release: 6 months ago - 1 dependent package - 41.4 thousand downloads total - 1 maintainer
BicARE 1.60.0
Biclustering Analysis and Results Exploration3 versions - Latest release: 6 months ago - 1 dependent package - 41.4 thousand downloads total - 1 maintainer
Top 7.8% on bioconductor.org
3 versions - Latest release: 6 months ago - 3 dependent packages - 36.6 thousand downloads total - 1 maintainer
flowDensity 1.36.1
Sequential Flow Cytometry Data Gating3 versions - Latest release: 6 months ago - 3 dependent packages - 36.6 thousand downloads total - 1 maintainer
ATACCoGAPS 1.4.0
Analysis Tools for scATACseq Data with CoGAPS3 versions - Latest release: 6 months ago - 1.55 thousand downloads total - 4 stars on GitHub - 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
systemPipeShiny 1.12.0
systemPipeShiny: An Interactive Framework for Workflow Management and Visualization3 versions - Latest release: 6 months ago - 4.34 thousand downloads total - 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
seqArchRplus 1.2.0
Downstream analyses of promoter sequence architectures and HTML report generation3 versions - Latest release: 6 months ago - 1.51 thousand downloads total - 0 stars on GitHub - 1 maintainer
flowCyBar 1.38.0
Analyze flow cytometric data using gate information3 versions - Latest release: 6 months ago - 16.4 thousand downloads total - 1 maintainer
Top 9.2% on bioconductor.org
3 versions - Latest release: 6 months ago - 27.9 thousand downloads total - 1 maintainer
MantelCorr 1.72.0
Compute Mantel Cluster Correlations3 versions - Latest release: 6 months ago - 27.9 thousand downloads total - 1 maintainer
Melissa 1.18.0
Bayesian clustering and imputationa of single cell methylomes3 versions - Latest release: 6 months ago - 5.54 thousand downloads total - 1 maintainer
TCseq 1.26.0
Time course sequencing data analysis3 versions - Latest release: 6 months ago - 16.3 thousand downloads total - 1 maintainer
flowCHIC 1.36.0
Analyze flow cytometric data using histogram information3 versions - Latest release: 6 months ago - 15.6 thousand downloads total - 1 maintainer
BEARscc 1.22.0
BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters)3 versions - Latest release: 6 months ago - 7.84 thousand downloads total - 1 maintainer
VaSP 1.14.0
Quantification and Visualization of Variations of Splicing in Population3 versions - Latest release: 6 months ago - 3.14 thousand downloads total - 3 stars on GitHub - 1 maintainer
survtype 1.18.0
Subtype Identification with Survival Data3 versions - Latest release: 6 months ago - 5.54 thousand downloads total - 1 maintainer
Related Keywords
Software
296
GeneExpression
114
Sequencing
91
Visualization
89
ImmunoOncology
84
SingleCell
74
RNASeq
74
DifferentialExpression
68
Classification
56
Transcriptomics
56
MultipleComparison
50
Microarray
48
Normalization
38
DataImport
37
Transcription
37
QualityControl
32
StatisticalMethod
30
GeneSetEnrichment
30
Network
29
Preprocessing
29
DimensionReduction
29
Proteomics
27
GraphAndNetwork
27
Bayesian
26
BiomedicalInformatics
26
FeatureExtraction
26
Regression
24
CellBasedAssays
23
FlowCytometry
23
SystemsBiology
22
CellBiology
21
Annotation
21
Genetics
20
Pathways
19
GO
19
TimeCourse
19
DataRepresentation
19
PrincipalComponent
17
Infrastructure
16
Epigenetics
15
BatchEffect
14
r
14
FunctionalGenomics
14
Metabolomics
12
Coverage
12
KEGG
11
ChIPSeq
11
GUI
10
mRNAMicroarray
10
GeneRegulation
10
GeneticVariability
10
SNP
9
bioconductor
9
Spatial
9
clustering
8
bioinformatics
8
Survival
8
DNAMethylation
8
Microbiome
8
DNASeq
7
AlternativeSplicing
7
DifferentialSplicing
7
OneChannel
7
MassSpectrometry
7
single-cell
7
Alignment
7
NetworkInference
7
Metagenomics
7
ReportWriting
7
Cheminformatics
6
SomaticMutation
6
ExperimentalDesign
6
ATACSeq
6
NetworkEnrichment
6
TwoChannel
6
transcriptomics
5
HiC
5
GenomicVariation
5
ExonArray
5
CopyNumberVariation
5
GenePrediction
5
AssayDomain
5
Pharmacogenomics
5
ShinyApps
5
Phylogenetics
5
Pharmacogenetics
5
DifferentialMethylation
5
r-package
4
MicroRNAArray
4
GeneTarget
4
human-cell-atlas
4
ProprietaryPlatforms
4
bioconductor-package
4
MethylSeq
4
MicrotitrePlateAssay
4
SupportVectorMachine
3
DecisionTree
3
MultipleSequenceAlignment
3
shiny
3
gene
3