Ecosyste.ms: Packages

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

bioconductor.org "SingleCell" keyword

Top 1.5% on bioconductor.org
scater 1.32.0
Single-Cell Analysis Toolkit for Gene Expression Data in R
4 versions - Latest release: 20 days ago - 96 dependent packages - 622 thousand downloads total - 1 maintainer
Top 0.6% on bioconductor.org
edgeR 4.2.0
Empirical Analysis of Digital Gene Expression Data in R
14 versions - Latest release: 20 days ago - 181 dependent packages - 3.02 million downloads total - 4 maintainers
Top 1.4% on bioconductor.org
HDF5Array 1.32.0
HDF5 backend for DelayedArray objects
4 versions - Latest release: 20 days ago - 54 dependent packages - 990 thousand downloads total - 1 maintainer
Top 1.0% on bioconductor.org
SingleCellExperiment 1.26.0
S4 Classes for Single Cell Data
3 versions - Latest release: 20 days ago - 201 dependent packages - 1.07 million downloads total - 1 maintainer
Top 4.7% on bioconductor.org
infercnv 1.18.1
Infer Copy Number Variation from Single-Cell RNA-Seq Data
4 versions - Latest release: 6 months ago - 80.3 thousand downloads total - 502 stars on GitHub - 1 maintainer
clustifyr 1.14.0
Classifier for Single-cell RNA-seq Using Cell Clusters
3 versions - Latest release: 7 months ago - 9.06 thousand downloads total - 101 stars on GitHub - 1 maintainer
DESpace 1.2.1
DESpace: a framework to discover spatially variable genes
4 versions - Latest release: 3 months ago - 1.47 thousand downloads total - 3 stars on GitHub - 1 maintainer
LineagePulse 1.21.0 removed
Differential expression analysis and model fitting for single-cell RNA-seq data
2 versions - Latest release: 6 months ago - 7.08 thousand downloads total - 11 stars on GitHub - 1 maintainer
infinityFlow 1.12.0
Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions
3 versions - Latest release: 6 months ago - 4.46 thousand downloads total - 1 maintainer
gemma.R 3.0.3
A wrapper for Gemma's Restful API to access curated gene expression data and differential express...
6 versions - Latest release: 7 days ago - 2.01 thousand downloads total - 9 stars on GitHub - 1 maintainer
VDJdive 1.6.0
Analysis Tools for 10X V(D)J Data
3 versions - Latest release: 23 days ago - 1.65 thousand downloads total - 6 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 4.4% on bioconductor.org
SingleR 2.6.0
Reference-Based Single-Cell RNA-Seq Annotation
4 versions - Latest release: 7 days ago - 5 dependent packages - 197 thousand downloads total - 162 stars on GitHub - 1 maintainer
OmnipathR 3.10.1
OmniPath web service client and more
3 versions - Latest release: 6 months ago - 3 dependent packages - 23.4 thousand downloads total - 1 maintainer
CyTOFpower 1.8.0
Power analysis for CyTOF experiments
3 versions - Latest release: 6 months ago - 2.32 thousand downloads total - 1 maintainer
velociraptor 1.14.0
Toolkit for Single-Cell Velocity
3 versions - Latest release: 22 days ago - 6.83 thousand downloads total - 51 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
deconvR 1.8.0
Simulation and Deconvolution of Omic Profiles
3 versions - Latest release: 6 months ago - 3.22 thousand downloads total - 9 stars on GitHub - 1 maintainer
scTreeViz 1.8.0
R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with h...
3 versions - Latest release: 6 months ago - 2.46 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
FEAST 1.10.0
FEAture SelcTion (FEAST) for Single-cell clustering
3 versions - Latest release: 6 months ago - 4.7 thousand downloads total - 9 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 analysis
3 versions - Latest release: 6 months ago - 10 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
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
Top 8.0% on bioconductor.org
TrajectoryUtils 1.10.1
Single-Cell Trajectory Analysis Utilities
4 versions - Latest release: 3 months ago - 5 dependent packages - 65.6 thousand downloads total - 1 maintainer
synapsis 1.8.0
An R package to automate the analysis of double-strand break repair during meiosis
3 versions - Latest release: 6 months ago - 2.18 thousand downloads total - 1 maintainer
scMultiSim 1.0.0
Simulation of Multi-Modality Single Cell Data Guided By Gene Regulatory Networks and Cell-Cell In...
1 version - Latest release: 22 days ago - 144 downloads total - 18 stars on GitHub - 1 maintainer
cydar 1.26.0
Using Mass Cytometry for Differential Abundance Analyses
3 versions - Latest release: 6 months ago - 13.2 thousand downloads total - 1 maintainer
scDD 1.26.0
Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions
3 versions - Latest release: 6 months ago - 1 dependent package - 19.2 thousand downloads total - 32 stars on GitHub - 1 maintainer
lute 1.0.0
Framework for cell size scale factor normalized bulk transcriptomics deconvolution experiments
1 version - Latest release: 22 days ago - 340 downloads total - 2 stars on GitHub - 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
concordexR 1.2.0
Calculate the concordex coefficient
3 versions - Latest release: 6 months ago - 1.67 thousand downloads total - 6 stars on GitHub - 1 maintainer
SPsimSeq 1.12.0
Semi-parametric simulation tool for bulk and single-cell RNA sequencing data
3 versions - Latest release: 6 months ago - 2 dependent packages - 5.36 thousand downloads total - 10 stars on GitHub - 1 maintainer
eds 1.4.0
eds: Low-level reader for Alevin EDS format
3 versions - Latest release: 6 months ago - 2 dependent packages - 13.5 thousand downloads total - 0 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
CeTF 1.14.0
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation an...
3 versions - Latest release: 6 months ago - 6.04 thousand downloads total - 1 maintainer
FLAMES 1.8.0
FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data
3 versions - Latest release: 6 months ago - 4.98 thousand downloads total - 7 stars on GitHub - 1 maintainer
miloR 2.0.0
Differential neighbourhood abundance testing on a graph
3 versions - Latest release: 21 days ago - 10.9 thousand downloads total - 310 stars on GitHub - 1 maintainer
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
treekoR 1.10.0
Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations
3 versions - Latest release: 6 months ago - 2.99 thousand downloads total - 1 maintainer
CAEN 1.10.0
Category encoding method for selecting feature genes for the classification of single-cell RNA-seq
3 versions - Latest release: 6 months ago - 2.78 thousand downloads total - 1 maintainer
scRepertoire 1.12.0
A toolkit for single-cell immune receptor profiling
3 versions - Latest release: 6 months ago - 19.4 thousand downloads total - 1 maintainer
Top 6.1% on bioconductor.org
clusterExperiment 2.22.0
Compare Clusterings for Single-Cell Sequencing
3 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 Analysis
3 versions - Latest release: 6 months ago - 6.46 thousand downloads total - 1 maintainer
phenopath 1.26.0
Genomic trajectories with heterogeneous genetic and environmental backgrounds
3 versions - Latest release: 6 months ago - 1 dependent package - 11 thousand downloads total - 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
mfa 1.24.0
Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations
3 versions - Latest release: 6 months ago - 1 dependent package - 10.8 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
SCArray 1.10.0
Large-scale single-cell omics data manipulation with GDS files
3 versions - Latest release: 6 months ago - 1 dependent package - 3.48 thousand downloads total - 1 stars on GitHub - 1 maintainer
BPRMeth 1.28.0
Model higher-order methylation profiles
3 versions - Latest release: 6 months ago - 1 dependent package - 11.9 thousand downloads total - 1 maintainer
aggregateBioVar 1.12.0
Differential Gene Expression Analysis for Multi-subject scRNA-seq
3 versions - Latest release: 6 months ago - 5.15 thousand downloads total - 5 stars on GitHub - 1 maintainer
HGC 1.10.0
A fast hierarchical graph-based clustering method
3 versions - Latest release: 6 months ago - 3.61 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
miRspongeR 2.6.0
Identification and analysis of miRNA sponge regulation
3 versions - Latest release: 6 months ago - 1 dependent package - 6.08 thousand downloads total - 5 stars on GitHub - 1 maintainer
scMET 1.4.0
Bayesian modelling of cell-to-cell DNA methylation heterogeneity
3 versions - Latest release: 6 months ago - 1.73 thousand downloads total - 18 stars on GitHub - 1 maintainer
immunoClust 1.34.0
immunoClust - Automated Pipeline for Population Detection in Flow Cytometry
3 versions - Latest release: 6 months ago - 13.4 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
ccfindR 1.22.0
Cancer Clone Finder
3 versions - Latest release: 6 months ago - 1 dependent package - 11.4 thousand downloads total - 1 maintainer
Dino 1.8.0
Normalization of Single-Cell mRNA Sequencing Data
3 versions - Latest release: 6 months ago - 2.77 thousand downloads total - 8 stars on GitHub - 1 maintainer
LRcell 1.10.0
Differential cell type change analysis using Logistic/linear Regression
3 versions - Latest release: 6 months ago - 3.04 thousand downloads total - 3 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: 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
cytoKernel 1.8.0
Differential expression using kernel-based score test
3 versions - Latest release: 6 months ago - 2.32 thousand downloads total - 0 stars on GitHub - 1 maintainer
POWSC 1.10.0
Simulation, power evaluation, and sample size recommendation for single cell RNA-seq
3 versions - Latest release: 6 months ago - 3.04 thousand downloads total - 1 maintainer
speckle 1.2.0
Statistical methods for analysing single cell RNA-seq data
3 versions - Latest release: 6 months ago - 2.91 thousand downloads total - 1 maintainer
FuseSOM 1.4.0
A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets
3 versions - Latest release: 6 months ago - 1.79 thousand downloads total - 1 stars on GitHub - 1 maintainer
MultimodalExperiment 1.2.0
Integrative Bulk and Single-Cell Experiment Container
3 versions - Latest release: 6 months ago - 1.15 thousand downloads total - 1 maintainer
scRecover 1.18.0
scRecover for imputation of single-cell RNA-seq data
3 versions - Latest release: 6 months ago - 5.98 thousand downloads total - 8 stars on GitHub - 1 maintainer
CancerInSilico 2.22.0
An R interface for computational modeling of tumor progression
3 versions - Latest release: 6 months ago - 8.93 thousand downloads total - 2 maintainers
ADImpute 1.12.0
Adaptive Dropout Imputer (ADImpute)
3 versions - Latest release: 6 months ago - 5.25 thousand downloads total - 0 stars on GitHub - 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
SIMD 1.20.0
Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site
3 versions - Latest release: 6 months ago - 5.7 thousand downloads total - 1 maintainer
Melissa 1.18.0
Bayesian clustering and imputationa of single cell methylomes
3 versions - Latest release: 6 months ago - 5.54 thousand downloads total - 1 maintainer
LinTInd 1.6.0
Lineage tracing by indels
3 versions - Latest release: 6 months ago - 2.06 thousand downloads total - 1 maintainer
miQC 1.10.0
Flexible, probabilistic metrics for quality control of scRNA-seq data
3 versions - Latest release: 6 months ago - 5.17 thousand downloads total - 16 stars on GitHub - 1 maintainer
NeuCA 1.8.1
NEUral network-based single-Cell Annotation tool
4 versions - Latest release: 2 months ago - 2.02 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
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
LoomExperiment 1.20.0
LoomExperiment container
3 versions - Latest release: 6 months ago - 2 dependent packages - 28.2 thousand downloads total - 1 maintainer
SCOPE 1.14.0
A normalization and copy number estimation method for single-cell DNA sequencing
3 versions - Latest release: 6 months ago - 4.8 thousand downloads total - 1 maintainer
singleCellTK 2.12.2
Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data
4 versions - Latest release: 3 months ago - 1 dependent package - 17.8 thousand downloads total - 1 maintainer
SCArray.sat 1.2.1
Large-scale single-cell RNA-seq data analysis using GDS files and Seurat
4 versions - Latest release: 4 months ago - 1.24 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
TRONCO 2.34.0
TRONCO, an R package for TRanslational ONCOlogy
3 versions - Latest release: 6 months ago - 16.6 thousand downloads total - 1 maintainer
peco 1.14.0
A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
3 versions - Latest release: 6 months ago - 4.1 thousand downloads total - 12 stars on GitHub - 1 maintainer
celaref 1.20.0
Single-cell RNAseq cell cluster labelling by reference
3 versions - Latest release: 6 months ago - 8.85 thousand downloads total - 1 maintainer
flowSpecs 1.16.0
Tools for processing of high-dimensional cytometry data
3 versions - Latest release: 6 months ago - 5.55 thousand downloads total - 6 stars on GitHub - 1 maintainer
methylscaper 1.10.0
Visualization of Methylation Data
3 versions - Latest release: 6 months ago - 2.84 thousand downloads total - 1 maintainer
TDbasedUFE 1.2.0
Tensor Decomposition Based Unsupervised Feature Extraction
3 versions - Latest release: 6 months ago - 1 dependent package - 1.75 thousand downloads total - 5 stars on GitHub - 1 maintainer
Cepo 1.8.0
Cepo for the identification of differentially stable genes
3 versions - Latest release: 6 months ago - 1 dependent package - 4.59 thousand downloads total - 1 maintainer
restfulSE 1.24.0
Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface
3 versions - Latest release: 6 months ago - 3 dependent packages - 10.6 thousand downloads total - 1 maintainer
mumosa 1.10.0
Multi-Modal Single-Cell Analysis Methods
3 versions - Latest release: 6 months ago - 3.74 thousand downloads total - 1 maintainer
tidySpatialExperiment 1.0.0
Brings SpatialExperiment to the tidyverse
2 versions - Latest release: 7 days ago - 347 downloads total - 4 stars on GitHub - 1 maintainer
TDbasedUFEadv 1.2.0
Advanced package of tensor decomposition based unsupervised feature extraction
3 versions - Latest release: 6 months ago - 1.55 thousand downloads total - 0 stars on GitHub - 1 maintainer
RGMQL 1.22.1
GenoMetric Query Language for R/Bioconductor
4 versions - Latest release: about 1 month ago - 6.14 thousand downloads total - 1 maintainer
scDDboost 1.4.0
A compositional model to assess expression changes from single-cell rna-seq data
3 versions - Latest release: 6 months ago - 1.63 thousand downloads total - 0 stars on GitHub - 1 maintainer
simpleSeg 1.6.0
A package to perform simple cell segmentation
4 versions - Latest release: 14 days ago - 1.88 thousand downloads total - 0 stars on GitHub - 1 maintainer
TrajectoryGeometry 1.10.1
This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns
4 versions - Latest release: 2 months ago - 2.54 thousand downloads total - 1 maintainer
ASURAT 1.6.0
Functional annotation-driven unsupervised clustering for single-cell data
3 versions - Latest release: 6 months ago - 2.49 thousand downloads total - 1 maintainer
Related Keywords
Software 284 GeneExpression 146 RNASeq 117 Sequencing 110 Transcriptomics 100 ImmunoOncology 94 Clustering 74 Visualization 61 DifferentialExpression 50 DataImport 48 Normalization 37 Preprocessing 36 DimensionReduction 36 Spatial 31 Classification 29 Transcription 28 QualityControl 25 DataRepresentation 25 Regression 25 CellBasedAssays 23 StatisticalMethod 20 Bayesian 20 MultipleComparison 20 FlowCytometry 19 Coverage 19 single-cell 19 Infrastructure 18 FeatureExtraction 17 CellBiology 17 Genetics 15 Proteomics 14 Network 14 BatchEffect 14 Annotation 13 r 13 GeneSetEnrichment 13 ATACSeq 13 Epigenetics 12 BiomedicalInformatics 12 bioconductor 11 bioinformatics 10 GeneRegulation 10 SystemsBiology 10 GraphAndNetwork 10 scrna-seq 9 bioconductor-package 9 single-cell-rna-seq 9 DNAMethylation 8 PrincipalComponent 8 DNASeq 8 GeneTarget 8 Alignment 8 Pathways 7 Microarray 7 FunctionalGenomics 7 GUI 7 MassSpectrometry 6 ChIPSeq 6 ExperimentalDesign 6 transcriptomics 5 NetworkInference 5 Technology 5 gene-expression 5 GeneSignaling 5 KEGG 5 visualization 4 DifferentialMethylation 4 DifferentialSplicing 4 BiologicalQuestion 4 TimeCourse 4 Survival 4 GenomeAnnotation 4 CopyNumberVariation 4 CRISPR 4 genomics 4 SupportVectorMachine 4 human-cell-atlas 4 OneChannel 4 ReportWriting 4 ShinyApps 4 WholeGenome 3 MethylationArray 3 bayesian 3 AlternativeSplicing 3 HiddenMarkovModel 3 ThirdPartyClient 3 WorkflowStep 3 rstats 3 deconvolution 3 clustering 3 PooledScreens 3 shiny 3 normalization 2 NeuralNetwork 2 SomaticMutation 2 tensor-decomposition 2 ResearchField 2 gene-expression-profiles 2 scrnaseq 2 mRNAMicroarray 2