Biocview "SingleCell"

10X Genomics Chromium
10X Genomics Chromium
10X Genomics Chromium
Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface
Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface
Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface
A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)
A complete analysis of single cell subpopulations, from identifying subpopulations to analysing their relationship (scGPS = single cell Global Predictions of Subpopulation)
A correlation-based method for quality filtering of single-cell RNAseq data
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq
A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq
AIPS : Absolute Inference of Patient Signatures
An alignment and integration method for single cell genomics
An alignment and integration method for single cell genomics
Analysis of Copy Number Variation in Single-Cell-Sequencing Data
Analysis of Copy Number Variation in Single-Cell-Sequencing Data
Analysis of RNA-Seq Count Data using Multiple Corespondence Analysis
A normalization and copy number estimation method for single-cell DNA sequencing
A normalization and copy number estimation method for single-cell DNA sequencing
An R interface for computational modeling of tumor progression
An R interface for computational modeling of tumor progression
An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples
An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples
A package to extract spatial features based on multiplex IF images
A package to extract spatial features based on multiplex IF images
A package to extract spatial features based on multiplex IF images
ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression
A search tool for single cell RNA-seq data by gene lists
A search tool for single cell RNA-seq data by gene lists
Assigning scRNA-seq to clone-of-origin using copy number from ultra-low-depth scDNA-seq
A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data
A tool for unsupervised projection of single cell RNA-seq data
A tool for unsupervised projection of single cell RNA-seq data
A toolkit for performing KNN-based statistics for flow and mass cytometry data
A toolkit for performing KNN-based statistics for flow and mass cytometry data
A toolkit for single-cell immune receptor profiling
AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)
AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)
Augmented functionality for analysis of epigenomic variance
Automated, probabilistic assignment of scRNA-seq to cell types
Automatic calculation of literature relevance of genes
Automatic calculation of literature relevance of genes
Automatic calculation of literature relevance of genes
Automatic calculation of literature relevance of genes
Bayesian Analysis of Single-Cell Sequencing data
Bayesian Analysis of Single-Cell Sequencing data
Bayesian clustering and imputationa of single cell methylomes
Bayesian clustering and imputationa of single cell methylomes
Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations
Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations
bcbio Single-Cell RNA-Seq
bcbio Single-Cell RNA-Seq
BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters)
BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters)
Cancer Clone Finder
Cancer Clone Finder
Casc
CB2: A cluster-based approach for distinguishing cells from background barcodes in 10x Genomics data
Cell Signalling Using Single Cell RNAseq Data Analysis
Cell Signalling Using Single Cell RNAseq Data Analysis
Cell type annotation for unannotated single-cell RNA-Seq data
CEllular Latent Dirichlet Allocation
CEllular Latent Dirichlet Allocation
CEllular Latent Dirichlet Allocation
Chromatin Variation Across Regions
Chromatin Variation Across Regions
CiteFuse: multi-modal analysis of CITE-seq data
CiteFuse: multi-modal analysis of CITE-seq data
Classifier for Single-cell RNA-seq Using Cell Clusters
Classifier for Single-cell RNA-seq Using Cell Clusters
Classifier for Single-cell RNA-seq Using Cell Clusters
Classifier for Single-cell RNA-seq Using Cell Clusters
Classifier for Single-cell RNA-seq Using Cell Clusters
Clone Identification from Single Cell Data
Clone Identification from Single Cell Data
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis
Compare Characteristic Features of Count Data Sets
Compare Characteristic Features of Count Data Sets
Compare Clusterings for Single-Cell Sequencing
Compare Clusterings for Single-Cell Sequencing
Compare Clusterings for Single-Cell Sequencing
Compute cell-type specific enrichments with high resolution
Condition Comparison in scRNA-seq Data
Condition Comparison in scRNA-seq Data
Correspondence Analysis for Single Cell Data
Cytometry dATa anALYSis Tools
Cytometry dATa anALYSis Tools
Deconvolution of Bulk Sequencing Experiments using Single Cell Data
DEsingle for detecting three types of differential expression in single-cell RNA-seq data
DEsingle for detecting three types of differential expression in single-cell RNA-seq data
Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition
Detection of cell-cell interaction from single-cell RNA-seq dataset by tensor decomposition
Determination of essential phenotypic elements of clusters in high-dimensional entities
Determination of essential phenotypic elements of clusters in high-dimensional entities
Differential discovery in high-dimensional cytometry via high-resolution clustering
Differential discovery in high-dimensional cytometry via high-resolution clustering
Differential expression analysis and model fitting for single-cell RNA-seq data
Differential expression analysis and model fitting for single-cell RNA-seq data
distinct: a method for differential analyses via hierarchical permutation tests
Dual redundant reference sequencing
Easy single cell analysis platform for enrichment
Evaluate Cellspecific Mixing
Evaluate Cellspecific Mixing
exploratory data analysis of tabula muris droplet counts
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data
Fast and accurate scRNA-seq cell type identification
Fast and accurate scRNA-seq cell type identification
Fast Correlation Based Filter for Feature Selection
Fast Correlation Based Filter for Feature Selection
Fast, Sensitive, and Accurate Integration of Single Cell Data
FCBF-based Co-Expression Networks for Single Cells
FCBF-based Co-Expression Networks for Single Cells
FCBF-based Co-Expression Networks for Single Cells
Find breakpoints in Strand-seq data
Find breakpoints in Strand-seq data
Find breakpoints in Strand-seq data
Fishpond: differential transcript and gene expression with inferential replicates
Fishpond: differential transcript and gene expression with inferential replicates
Fit a Gamma-Poisson Generalized Linear Model
Fit a Gamma-Poisson Generalized Linear Model
Functional interpretation of single cell RNA-seq latent manifolds
Functional interpretation of single cell RNA-seq latent manifolds
Functions to conduct quality control analysis in methylation data
Functions to conduct quality control analysis in methylation data
Generate QC Reports For Alevin Output
Generate QC Reports For Alevin Output
Generating Tree Hierarchy Visualizations from Gene Expression Data
Generating Tree Hierarchy Visualizations from Gene Expression Data
GenoMetric Query Language for R/Bioconductor
GenoMetric Query Language for R/Bioconductor
Genomic trajectories with heterogeneous genetic and environmental backgrounds
HDF5 backend for DelayedArray objects
HDF5 backend for DelayedArray objects
Heterogeneity-Induced Pre-Processing tOol
Heterogeneity-Induced Pre-Processing tOol
Hexbin plots for single cell omics data
Hexbin plots for single cell omics data
Identify genes associated with multiple expression phenotypes in single-cell CRISPR screening data
Identify genes associated with multiple expression phenotypes in single-cell CRISPR screening data
ILoReg enables high-precision cell population identification from scRNA-Seq data
immunoClust - Automated Pipeline for Population Detection in Flow Cytometry
Improving replicability in single-cell RNA-Seq cell type discovery
Improving replicability in single-cell RNA-Seq cell type discovery
Indentification of significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data
Indentification of significantly activated ligand-receptor interactions across clusters of cells from single-cell RNA sequencing data
Infer Copy Number Variation from Single-Cell RNA-Seq Data
Infer Copy Number Variation from Single-Cell RNA-Seq Data
Infer Copy Number Variation from Single-Cell RNA-Seq Data
Inference of Chromosome-length Haplotypes using Genomic Data of Single Gamete Cells
Inference of Chromosome-Length Haplotypes Using Genomic Data of Single Gamete Cells
In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data
In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data
Interactive Analysis of Single Cell RNA-Seq Data
Interactive Analysis of Single Cell RNA-Seq Data
Interactive Analysis of Single Cell RNA-Seq Data
Interactive SummarizedExperiment Explorer
Interactive SummarizedExperiment Explorer
Interactive SummarizedExperiment Explorer
Interactive SummarizedExperiment Explorer
Interactive visualization of scRNA-seq data with Cerebro
Interpretable marker-based single-cell pseudotime using Bayesian parametric models
Interpretable marker-based single-cell pseudotime using Bayesian parametric models
iSEE Universe
iSEE Universe
iSEE Universe
kallisto | bustools R utilities
kallisto | bustools R utilities
kallisto | bustools R utilities
Landscape Single Cell Entropy
Learn and Apply Cell Type Signatures
Learn and Apply Cell Type Signatures
Linear model and normality based normalization and transformation method (Linnorm)
Longitudinal Analysis of Cancer Evolution (LACE)
Longitudinal Analysis of Cancer Evolution (LACE)
LoomExperiment container
LoomExperiment container
Manipulate Zarr archives as R objects
Merging of phenotype information from different cytometric profiles
Methods for Single-Cell RNA-Seq Data Analysis
Methods for Single-Cell RNA-Seq Data Analysis
Mine Associated Gene Expressions (from single-cell Rna Seq data)
Mini-batch K-means Clustering for Single-Cell RNA-seq
Mini-batch K-means Clustering for Single-Cell RNA-seq
Minimized Single-Cell Consensus Clustering
Minimized Single-Cell Consensus Clustering
Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions
Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions
Mixture Nested Effects Models
Mixture Nested Effects Models
Model-based Analysis of Single Cell Transcriptomics
Model-based Analysis of Single Cell Transcriptomics
Model higher-order methylation profiles
Model higher-order methylation profiles
Multi-Contrast Gene Set Enrichment Analysis
Multi-Contrast Gene Set Enrichment Analysis
Multi-Contrast Gene Set Enrichment Analysis
Multi-sample multi-group scRNA-seq data analysis tools
Multi-sample multi-group scRNA-seq data analysis tools
Multi-sample multi-group scRNA-seq data analysis tools
Network smoothing for scRNAseq
Network smoothing for scRNAseq
Normalization of single cell RNA-seq data
Normalization of single cell RNA-seq data
ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics
ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics
PCAtools: Everything Principal Components Analysis
PhantomPurgeR
Phenotypic EMD for comparison of single-cell samples
Phenotypic EMD for comparison of single-cell samples
Phenotypic EMD for comparison of single-cell samples
pipeline for single cell RNA-seq data analysis
pipeline for single cell RNA-seq data analysis
PolyA counting and differential transcript usage analysis for scRNA-seq data
Precict cis-co-accessibility from single-cell chromatin accessibility data
Precict cis-co-accessibility from single-cell chromatin accessibility data
Precict cis-co-accessibility from single-cell chromatin accessibility data
R/Bioconductor package to manage hierarchies in genomic datasets
R/Bioconductor package to manage hierarchies in genomic datasets
Reconstruction, visualization and analysis of branching trajectories
Reconstruction, visualization and analysis of branching trajectories
Reconstruction, visualization and analysis of branching trajectories
Reference-Based Single-Cell RNA-Seq Annotation
Reference-Based Single-Cell RNA-Seq Annotation
Reference Index for Cell Types
S4 Classes for Single Cell Data
S4 Classes for Single Cell Data
S4 Classes for Single Cell Data
S4 Class for segmented spatial 'omics data
SAFE-clustering:Single-cell Aggregated (From Ensemble) Clustering for Single-cell RNA-seq Data
SAME: Single-cell RNA-seq Aggregated clustering via Mixture model Ensemble for Single-cell RNA-seq Data
scClassify: single-cell Hierarchical Classification
scClassify: single-cell Hierarchical Classification
scDataviz: single cell dataviz and downstream analyses
scDataviz: single cell dataviz and downstream analyses
scDblFinder
scDblFinder
SCENIC (Single Cell rEgulatory Network Inference and Clustering)
scMerge: Merging multiple batches of scRNA-seq data
scMerge: Merging multiple batches of scRNA-seq data
scRecover for imputation of single-cell RNA-seq data
scRecover for imputation of single-cell RNA-seq data
scRecover for imputation of single-cell RNA-seq data
scRMD: Imputation for single cell RNA-seq data via robust matrix decomposition
scRMD: Imputation for single cell RNA-seq data via robust matrix decomposition
Semi-parametric simulation tool for bulk and single-cell RNA sequencing data
SIMLR: Single-cell Interpretation via Multi-kernel LeaRning
Simple Simulation of Single-cell RNA Sequencing Data
Simple Simulation of Single-cell RNA Sequencing Data
Simple Simulation of Single-cell RNA Sequencing Data
Simple Simulation of Single-cell RNA Sequencing Data
SINCE - a robust algorithm for single-cell number of clusters estimation
Single-cell analysis toolkit for gene expression data in R
Single-Cell Analysis Toolkit for Gene Expression Data in R
Single-Cell Analysis Toolkit for Gene Expression Data in R
Single-Cell Batch Correction Methods
Single-Cell Batch Correction Methods
Single-Cell Consensus Clustering
Single-Cell Consensus Clustering
single-cell higher order testing
single-cell higher order testing
Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)
Single-Cell Operation for Neat Enrichment
Single Cell Overview of Normalized Expression data
Single Cell Overview of Normalized Expression data
Single cell replicability analysis
Single cell replicability analysis
Single-cell RNAseq cell cluster labelling by reference
Single-cell RNAseq cell cluster labelling by reference
Single-cell RNA-seq toolkit
Single-cell RNA-seq toolkit
Single-cell RNA sequencing data normalization
Single-cell RNA sequencing data normalization
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single Cell RNA-Seq UMI Filtering Facilitator (scruff)
Single-Cell RNA-Seq Utilities
Single-Cell RNA-Seq Utilities
Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data
Small-Count Analysis Methods for High-Dimensional Data
Small-Count Analysis Methods for High-Dimensional Data
SMNN: Batch Effect Correction for Single-cell RNA-seq data with Supervised Mutual Nearest Neighbor Detection
Spatial analysis of in situ cytometry data
Spatial analysis of in situ cytometry data
Spatial Reconstruction of Tissues from scRNA-seq Data
Spatial Transcriptomics Analysis
Spatial Transcriptomics Analysis
Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site
Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site
Statistical tests for detecting differential distributions based on the 2-Wasserstein distance
Statistical tests for detecting differential distributions based on the 2-Wasserstein distance
Statistical tests for detecting differential distributions based on the 2-Wasserstein distance
Subread Sequence Alignment and Counting for R
Survival of patients using ors on TCGA data
Switch-like differential expression across single-cell trajectories
Switch-like differential expression across single-cell trajectories
Targeted scRNA-seq primer design for TAP-seq
Targeted scRNA-seq primer design for TAP-seq
Tools for ordering single-cell sequencing
Tools for ordering single-cell sequencing
Tools for processing of high-dimensional cytometry data
Tools for processing of high-dimensional cytometry data
trajectory-based differential expression analysis for sequencing data
trajectory-based differential expression analysis for sequencing data
Transcript Quantification Import with Automatic Metadata
Transcript Quantification Import with Automatic Metadata
Tree Aggregation
TRONCO, an R package for TRanslational ONCOlogy
TRONCO, an R package for TRanslational ONCOlogy
Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis
Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis
User Friendly Single-Cell and Bulk RNA Sequencing Visualization
User Friendly Single-Cell and Bulk RNA Sequencing Visualization
User Friendly Single-Cell and Bulk RNA Sequencing Visualization
Using Mass Cytometry for Differential Abundance Analyses
Using Mass Cytometry for Differential Abundance Analyses
Utilities for Handling Single-Cell Droplet Data
Utilities for Handling Single-Cell Droplet Data
Varying-Censoring Aware Matrix Factorization
Visualization of highly multiplexed imaging cytometry data in R
Visualization of highly multiplexed imaging cytometry data in R
Visualization of highly multiplexed imaging cytometry data in R
Weighted matrix manipulation, finding components of variation with weighted or sparse data
Weighted matrix manipulation, finding components of variation with weighted or sparse data
What the Package Does TODOELI
Wind: weighted indexes for clustering evaluation
Zero-Inflated Negative Binomial Model for RNA-Seq Data
Zero-Inflated Negative Binomial Model for RNA-Seq Data