Ecosyste.ms: Packages

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

bioconductor.org "DimensionReduction" keyword

matter 2.6.1
Scientific computing for out-of-memory signals and images
5 versions - Latest release: 9 days ago - 2 dependent packages - 19 thousand downloads total - 52 stars on GitHub - 1 maintainer
schex 1.16.1
Hexbin plots for single cell omics data
4 versions - Latest release: 4 months ago - 3 dependent packages - 13.8 thousand downloads total - 71 stars on GitHub - 1 maintainer
Top 9.3% on bioconductor.org
BiocSingular 1.20.0
Singular Value Decomposition for Bioconductor Packages
3 versions - Latest release: 20 days ago - 28 dependent packages - 702 thousand downloads total - 6 stars on GitHub - 1 maintainer
CelliD 1.10.1
Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis
4 versions - Latest release: 5 months ago - 9.32 thousand downloads total - 1 maintainer
autonomics 1.12.0
Unified statistal Modeling of Omics Data
4 versions - Latest release: 15 days ago - 3.18 thousand downloads total - 3 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
tenXplore 1.24.0
ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics
3 versions - Latest release: 6 months ago - 8.35 thousand downloads total - 1 maintainer
netboost 2.10.0
Network Analysis Supported by Boosting
3 versions - Latest release: 6 months ago - 4.72 thousand downloads total - 1 maintainer
IRISFGM 1.10.0
Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq
3 versions - Latest release: 6 months ago - 3 thousand downloads total - 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
RCM 1.18.0
Fit row-column association models with the negative binomial distribution for the microbiome
3 versions - Latest release: 6 months ago - 5.89 thousand downloads total - 1 maintainer
combi 1.14.0
Compositional omics model based visual integration
3 versions - Latest release: 6 months ago - 4.47 thousand downloads total - 0 stars on GitHub - 1 maintainer
STATegRa 1.38.0
Classes and methods for multi-omics data integration
3 versions - Latest release: 6 months ago - 15.5 thousand downloads total - 2 maintainers
scTensor 2.12.0
Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition
3 versions - Latest release: 6 months ago - 8.77 thousand downloads total - 1 maintainer
CoGAPS 3.22.0
Coordinated Gene Activity in Pattern Sets
3 versions - Latest release: 6 months ago - 3 dependent packages - 29.2 thousand downloads total - 4 maintainers
fmrs 1.12.0
Variable Selection in Finite Mixture of AFT Regression and FMR Models
3 versions - Latest release: 6 months ago - 5.47 thousand downloads total - 3 stars on GitHub - 1 maintainer
DelayedTensor 1.8.0
R package for sparse and out-of-core arithmetic and decomposition of Tensor
3 versions - Latest release: 6 months ago - 2.52 thousand downloads total - 4 stars on GitHub - 1 maintainer
slalom 1.24.0
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
3 versions - Latest release: 6 months ago - 9.37 thousand downloads total - 1 maintainer
scTGIF 1.16.0
Cell type annotation for unannotated single-cell RNA-Seq data
3 versions - Latest release: 6 months ago - 1 dependent package - 6.23 thousand downloads total - 1 maintainer
corral 1.12.0
Correspondence Analysis for Single Cell Data
3 versions - Latest release: 6 months ago - 5.22 thousand downloads total - 1 maintainer
MatrixQCvis 1.10.0
Shiny-based interactive data-quality exploration for omics data
3 versions - Latest release: 6 months ago - 4.12 thousand downloads total - 1 maintainer
CellTrails 1.20.0
Reconstruction, visualization and analysis of branching trajectories
3 versions - Latest release: 6 months ago - 6.81 thousand downloads total - 1 maintainer
Pigengene 1.28.0
Infers biological signatures from gene expression data
3 versions - Latest release: 6 months ago - 1 dependent package - 13.6 thousand downloads total - 1 maintainer
gep2pep 1.22.0
Creation and Analysis of Pathway Expression Profiles (PEPs)
3 versions - Latest release: 6 months ago - 7.44 thousand downloads total - 1 maintainer
scBFA 1.16.0
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile...
3 versions - Latest release: 6 months ago - 5.39 thousand downloads total - 1 maintainer
scry 1.14.0
Small-Count Analysis Methods for High-Dimensional Data
3 versions - Latest release: 6 months ago - 10.8 thousand downloads total - 1 maintainer
ATACCoGAPS 1.4.0
Analysis Tools for scATACseq Data with CoGAPS
3 versions - Latest release: 6 months ago - 1.55 thousand downloads total - 4 stars on GitHub - 1 maintainer
cellity 1.30.0
Quality Control for Single-Cell RNA-seq Data
3 versions - Latest release: 6 months ago - 13.4 thousand downloads total - 1 maintainer
veloviz 1.8.0
VeloViz: RNA-velocity informed 2D embeddings for visualizing cell state trajectories
3 versions - Latest release: 6 months ago - 2.57 thousand downloads total - 1 maintainer
weitrix 1.14.0
Tools for matrices with precision weights, test and explore weighted or sparse data
3 versions - Latest release: 6 months ago - 4.22 thousand downloads total - 1 maintainer
BiocSklearn 1.24.0
interface to python sklearn via Rstudio reticulate
3 versions - Latest release: 6 months ago - 15.9 thousand downloads total - 1 maintainer
globalSeq 1.30.0
Global Test for Counts
3 versions - Latest release: 6 months ago - 10.4 thousand downloads total - 1 stars on GitHub - 1 maintainer
DepecheR 1.18.0
Determination of essential phenotypic elements of clusters in high-dimensional entities
3 versions - Latest release: 6 months ago - 1 dependent package - 16 thousand downloads total - 1 maintainer
esetVis 1.28.2
Visualizations of expressionSet Bioconductor object
4 versions - Latest release: 4 months ago - 12.3 thousand downloads total - 1 maintainer
missRows 1.22.0
Handling Missing Individuals in Multi-Omics Data Integration
3 versions - Latest release: 6 months ago - 6.95 thousand downloads total - 1 maintainer
AffiXcan 1.20.0
A Functional Approach To Impute Genetically Regulated Expression
3 versions - Latest release: 6 months ago - 7.22 thousand downloads total - 1 maintainer
snifter 1.12.0
R wrapper for the python openTSNE library
3 versions - Latest release: 6 months ago - 1 dependent package - 13.7 thousand downloads total - 1 maintainer
rnaEditr 1.12.0
Statistical analysis of RNA editing sites and hyper-editing regions
3 versions - Latest release: 6 months ago - 3.35 thousand downloads total - 3 stars on GitHub - 1 maintainer
oneSENSE 1.24.0
One-Dimensional Soli-Expression by Nonlinear Stochastic Embedding (OneSENSE)
3 versions - Latest release: 6 months ago - 6.71 thousand downloads total - 1 maintainer
phemd 1.18.0
Phenotypic EMD for comparison of single-cell samples
3 versions - Latest release: 6 months ago - 5.54 thousand downloads total - 1 maintainer
ssPATHS 1.16.0
ssPATHS: Single Sample PATHway Score
3 versions - Latest release: 6 months ago - 4.47 thousand downloads total - 1 maintainer
lemur 1.0.5
Latent Embedding Multivariate Regression
6 versions - Latest release: 4 months ago - 1.2 thousand downloads total - 69 stars on GitHub - 1 maintainer
tricycle 1.10.0
tricycle: Transferable Representation and Inference of cell cycle
3 versions - Latest release: 6 months ago - 1 dependent package - 7.04 thousand downloads total - 15 stars on GitHub - 1 maintainer
PIUMA 1.0.0
Phenotypes Identification Using Mapper from topological data Analysis
1 version - Latest release: 21 days ago - 136 downloads total - 4 stars on GitHub - 1 maintainer
Banksy 1.0.0
Spatial transcriptomic clustering
1 version - Latest release: 21 days ago - 390 downloads total - 45 stars on GitHub - 1 maintainer
netSmooth 1.24.0
Network smoothing for scRNAseq
3 versions - Latest release: 7 days ago - 1 dependent package - 8.4 thousand downloads total - 26 stars on GitHub - 1 maintainer
qmtools 1.8.0
Quantitative Metabolomics Data Processing Tools
3 versions - Latest release: 7 days ago - 2.05 thousand downloads total - 1 stars on GitHub - 1 maintainer
Top 1.5% on bioconductor.org
scater 1.32.0
Single-Cell Analysis Toolkit for Gene Expression Data in R
4 versions - Latest release: 19 days ago - 96 dependent packages - 621 thousand downloads total - 1 maintainer
retrofit 1.4.0
RETROFIT: Reference-free deconvolution of cell mixtures in spatial transcriptomics
3 versions - Latest release: 20 days ago - 1.07 thousand downloads total - 4 stars on GitHub - 1 maintainer
RCSL 1.12.0
Rank Constrained Similarity Learning for single cell RNA sequencing data
4 versions - Latest release: 8 days ago - 2.76 thousand downloads total - 2 stars on GitHub - 1 maintainer
Top 5.2% on bioconductor.org
GENESIS 2.34.0
GENetic EStimation and Inference in Structured samples (GENESIS): Statistical methods for analyzi...
3 versions - Latest release: 9 days ago - 1 dependent package - 55.1 thousand downloads total - 32 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
pcaExplorer 2.30.0
Interactive Visualization of RNA-seq Data Using a Principal Components Approach
3 versions - Latest release: 20 days ago - 2 dependent packages - 49.4 thousand downloads total - 52 stars on GitHub - 1 maintainer
iSEEu 1.15.1
iSEE Universe
3 versions - Latest release: 20 days ago - 1 dependent package - 6.84 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 5.5% on bioconductor.org
iSEE 2.16.0
Interactive SummarizedExperiment Explorer
3 versions - Latest release: 20 days ago - 8 dependent packages - 33.6 thousand downloads total - 218 stars on GitHub - 1 maintainer
ggspavis 1.9.10
Visualization functions for spatial transcriptomics data
4 versions - Latest release: 20 days ago - 1 dependent package - 4.38 thousand downloads total - 1 stars on GitHub - 1 maintainer
ggsc 1.2.0
Visualizing Single Cell and Spatial Transcriptomics
3 versions - Latest release: 10 days ago - 930 downloads total - 30 stars on GitHub - 1 maintainer
POMA 1.14.0
Tools for Omics Data Analysis
3 versions - Latest release: 11 days ago - 1 dependent package - 4.86 thousand downloads total - 10 stars on GitHub - 1 maintainer
Top 4.4% on bioconductor.org
SC3 1.32.0
Single-Cell Consensus Clustering
3 versions - Latest release: 12 days ago - 4 dependent packages - 63.4 thousand downloads total - 115 stars on GitHub - 1 maintainer
timeOmics 1.16.0
Time-Course Multi-Omics data integration
3 versions - Latest release: 13 days ago - 1 dependent package - 5.04 thousand downloads total - 21 stars on GitHub - 1 maintainer
iNETgrate 1.2.0
Integrates DNA methylation data with gene expression in a single gene network
2 versions - Latest release: 13 days ago - 970 downloads total - 65 stars on GitHub - 1 maintainer
Top 5.4% on bioconductor.org
densvis 1.14.0
Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction
4 versions - Latest release: 13 days ago - 1 dependent package - 83.2 thousand downloads total - 1 maintainer
Top 5.9% on bioconductor.org
zinbwave 1.26.0
Zero-Inflated Negative Binomial Model for RNA-Seq Data
3 versions - Latest release: 13 days ago - 6 dependent packages - 83.5 thousand downloads total - 41 stars on GitHub - 1 maintainer
Top 5.6% on bioconductor.org
RDRToolbox 1.54.0
A package for nonlinear dimension reduction with Isomap and LLE.
3 versions - Latest release: 13 days ago - 42.3 thousand downloads total - 1 maintainer
Top 3.9% on bioconductor.org
made4 1.78.0
Multivariate analysis of microarray data using ADE4
3 versions - Latest release: 13 days ago - 1 dependent package - 85.8 thousand downloads total - 1 maintainer
CytoMDS 1.0.0
Low Dimensions projection of cytometry samples
1 version - Latest release: 21 days ago - 233 downloads total - 2 stars on GitHub - 1 maintainer
Top 8.4% on bioconductor.org
MOFA2 1.14.0
Multi-Omics Factor Analysis v2
4 versions - Latest release: 14 days ago - 22.5 thousand downloads total - 271 stars on GitHub - 1 maintainer
seqArchR 1.8.0
Identify Different Architectures of Sequence Elements
3 versions - Latest release: 16 days ago - 1 dependent package - 2.62 thousand downloads total - 1 stars on GitHub - 1 maintainer
gcatest 2.4.0
Genotype Conditional Association TEST
3 versions - Latest release: 16 days ago - 10.7 thousand downloads total - 5 stars on GitHub - 1 maintainer
Top 6.9% on bioconductor.org
lfa 2.4.0
Logistic Factor Analysis for Categorical Data
3 versions - Latest release: 16 days ago - 1 dependent package - 39.3 thousand downloads total - 15 stars on GitHub - 1 maintainer
Top 6.9% on bioconductor.org
M3Drop 1.30.0
Michaelis-Menten Modelling of Dropouts in single-cell RNASeq
3 versions - Latest release: 18 days ago - 1 dependent package - 40.7 thousand downloads total - 27 stars on GitHub - 1 maintainer
APL 1.8.0
Association Plots
4 versions - Latest release: 19 days ago - 2.83 thousand downloads total - 15 stars on GitHub - 1 maintainer
glmSparseNet 1.22.0
Network Centrality Metrics for Elastic-Net Regularized Models
4 versions - Latest release: 20 days ago - 8.83 thousand downloads total - 3 stars on GitHub - 1 maintainer
PLSDAbatch 1.0.0
PLSDA-batch
1 version - Latest release: 21 days ago - 186 downloads total - 10 stars on GitHub - 1 maintainer
iSEEfier 1.0.0
Streamlining the creation of initial states for starting an iSEE instance
1 version - Latest release: 21 days ago - 73 downloads total - 0 stars on GitHub - 1 maintainer
tpSVG 0.99.7
Thin plate models to detect spatially variable genes
1 version - Latest release: 21 days ago - 151 downloads total - 0 stars on GitHub - 1 maintainer
ClustAll 1.0.0
ClustAll: Data driven strategy to find groups of patients within complex diseases
1 version - Latest release: 21 days ago - 110 downloads total - 1 maintainer
RAIDS 1.0.0
Accurate Inference of Genetic Ancestry from Cancer Sequences
1 version - Latest release: 7 months ago - 708 downloads total - 5 stars on GitHub - 1 maintainer
SGCP 1.2.0
SGCP: A semi-supervised pipeline for gene clustering using self-training approach in gene co-expr...
2 versions - Latest release: 6 months ago - 1.77 thousand downloads total - 1 stars on GitHub - 1 maintainer
pathwayPCA 1.18.0
Integrative Pathway Analysis with Modern PCA Methodology and Gene Selection
2 versions - Latest release: 6 months ago - 1 dependent package - 7.17 thousand downloads total - 11 stars on GitHub - 1 maintainer
ILoReg 1.12.1
ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data
3 versions - Latest release: 3 months ago - 3.23 thousand downloads total - 4 stars on GitHub - 1 maintainer
Top 7.7% on bioconductor.org
Nebulosa 1.12.1
Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation
3 versions - Latest release: about 2 months ago - 34.7 thousand downloads total - 63 stars on GitHub - 1 maintainer
Related Keywords
Software 81 GeneExpression 38 SingleCell 36 Transcriptomics 35 Visualization 33 Clustering 29 RNASeq 28 PrincipalComponent 23 Sequencing 20 ImmunoOncology 19 Classification 13 Regression 13 Transcription 13 StatisticalMethod 11 Normalization 11 DifferentialExpression 11 FeatureExtraction 11 DataRepresentation 11 Preprocessing 10 QualityControl 9 GUI 8 Metabolomics 7 Network 7 GraphAndNetwork 7 MultipleComparison 7 Microarray 6 GeneSetEnrichment 6 Survival 5 SystemsBiology 5 Spatial 5 DataImport 5 Epigenetics 5 BiomedicalInformatics 5 Proteomics 5 Infrastructure 4 CellBasedAssays 4 single-cell 4 Genetics 4 GenomeWideAssociation 4 SNP 4 Pathways 4 human-cell-atlas 4 ShinyApps 4 BatchEffect 4 r-package 4 Bayesian 4 bioinformatics 3 FlowCytometry 3 GeneticVariability 3 single-cell-rna-seq 3 GenePrediction 3 Metagenomics 3 r 3 Microbiome 3 clustering 3 TimeCourse 3 KEGG 3 user-friendly 2 shiny 2 DNAMethylation 2 bioconductor 2 hacktoberfest 2 rna-seq 2 multi-omics 2 mRNAMicroarray 2 dimension-reduction 2 genomics 2 MultidimensionalScaling 2 SupportVectorMachine 2 NetworkInference 2 DecisionTree 2 FunctionalGenomics 2 WholeGenome 2 BiologicalQuestion 2 MassSpectrometry 2 MathematicalBiology 2 GeneRegulation 2 ATACSeq 2 GeneTarget 2 bioconductor-package 2 sequence-architectures 1 unsupervised-machine-learning 1 self-training 1 sequence-analysis 1 scikit-learn 1 promoter-sequence-architectures 1 nonnegative-matrix-factorization 1 nmf 1 MotifDiscovery 1 single-cell-analysis 1 DNASeq 1 mofa 1 factor-analysis 1 cran 1 core-services 1 single-cell-multiomics 1 networks 1 networkclustering 1 graphs 1 semi-supervised-learning 1