Biocview "SingleCell"

10X Genomics Chromium

Access matrix-like HDF5 server content or BigQuery content through a SummarizedExperiment interface

Acid Genomics Single Cell Experiment

A collection of single-cell V(D)J tools

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

Adaptive Dropout Imputer (ADImpute)

A dimensionality reduction tool using gene detection pattern to mitigate noisy expression profile of scRNA-seq

A fast hierarchical graph-based clustering method

AIPS : Absolute Inference of Patient Signatures

Algorithms and data structures for large single-cell expression matrices

An alignment and integration method for single cell genomics

Analysis of Copy Number Variation in Single-Cell-Sequencing Data

Analysis of Single-Cell CRISPR Screen Data

Analysis of single-cell epigenomics datasets with a Shiny App

Analysis Tools for 10X V(D)J Data

Analysis Tools for scATACseq Data with CoGAPS

Analyze gene therapy vector insertion sites data identified from genomics next generation sequencing reads for clonal tracking studies

Analyze High-dimensional Cytometry Data Using Tidy Data Principles

An Easy-to-use Systematic pipeline for ATACseq data analysis

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 python subsampling/sketching algorithms

An R Package for Integrating and Visualizing Single-Cell and Bulk Data to Resolve Regulatory Elements

An R package for quantitative integration and analysis of multiple omics assays from heterogeneous samples

An R package to automate the analysis of double-strand break repair during meiosis

A package to extract spatial features based on multiplex IF images

A pipeline especially built for computing several single-cell datasets

A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

ascend - Analysis of Single Cell Expression, Normalisation, and Differential expression

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

Association Plots

a statistical framework for differential pseudotime analysis in multiple single-cell RNA-seq samples

A Statistical Framework for Modeling and Identifying Differential Distributions in Single-cell RNA-sequencing Data

A Supervised Approach for **P**r**e**dicting **c**ell Cycle Pr**o**gression using scRNA-seq data

A Supervised Approach for Predicting Cell Cycle Progression Using Single-Cell RNA-seq Data

Asymmetric Within-Sample Transformation

ATACtion is the ACTIONet extension for sc/sn-ATAC-seq data analysis

A Tool for Generic Cell Type Enrichment Analysis

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 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)

Augmented functionality for analysis of epigenomic variance

Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions

Automated ingestion and conversion of various single-cell data formats.

Automated, probabilistic assignment of scRNA-seq to cell types

Automatic calculation of literature relevance of genes

A wrapper for Gemma's Restful API to access curated gene expression data and differential expression analyses

Barycenter Single-Cell Differential Expression for Case-Control Studies

Bayesian Analysis of Single-Cell Sequencing data

Bayesian clustering and imputationa of single cell methylomes

Bayesian hierarchical mixture of factor analyzers for modelling genomic bifurcations

Bayesian modelling of cell-to-cell DNA methylation heterogeneity

BEARscc (Bayesian ERCC Assesstment of Robustness of Single Cell Clusters)

Brings SingleCellExperiment to the Tidyverse

Browse the Human Cell Atlas data portal

Cancer Clone Finder

Casc

Category encoding method for selecting feature genes for the classification of single-cell RNA-seq

CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data

ccImpute: an accurate and scalable consensus clustering based approach to impute dropout events in the single-cell RNA-seq data

ccImpute: an accurate and scalable consensus clustering based approach to impute dropout events in the single-cell RNA-seq data (https://doi.org/10.1186/s12859-022-04814-8)

CellRanger Input/Output

Cell Signalling Using Single Cell RNAseq Data Analysis

Cell type annotation for unannotated single-cell RNA-Seq data

CEllular Latent Dirichlet Allocation

Cepo for the identification of differentially stable genes

Characterising single circulating tumor cell transcriptomes

Chromatin Variation Across Regions

CIMICE-R: (Markov) Chain Method to Inferr Cancer Evolution

CiteFuse: multi-modal analysis of CITE-seq data

Classifier for Single-cell RNA-seq Using Cell Clusters

Clonal Population Identification in Single-Cell RNA-Seq Data using Mitochondrial and Somatic Mutations

Clone Identification from Single Cell Data

Clustering Algorithms for Bioconductor

Clustering and Resolution Enhancement of Spatial Transcriptomes

Clustering Deviation Index (CDI)

Clustering, Differential Expression, and Trajectory Analysis for Single-Cell RNA-Seq

Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis

COexpression Tables ANalysis

Compare Characteristic Features of Count Data Sets

Compare Clusterings for Single-Cell Sequencing

Comprehensive Analysis of Gene Interactivity Networks Based on Single-Cell RNA-Seq

Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Compute cell-type specific enrichments with high resolution

Conditional Differential Analysis for Flow and Mass Cytometry Experiments

Condition Comparison in scRNA-seq Data

Construct Benchmarks for Single Cell Analysis Methods

Conversion Between scRNA-seq Objects

Conversion of single cell experiment output files to relational database

CopyKit

Correspondence Analysis for Single Cell Data

Create Interactive Single-cell Visualizations with the 'Vitessce' JavaScript Library

Creates hatched patterns for scatterplots

Crossover analysis and genetic map construction

Cytometry Cluster Hierarchy and Cellular-to-phenotype Associations

Cytometry dATa anALYSis Tools

Data structures, clustering and testing for single cell immune receptor repertoires (scRNAseq RepSeq/AIRR-seq)

Deconvolution of Bulk Sequencing Experiments using Single Cell Data

Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction

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

Detect marker panel from scRNA-seq profile

Determination of essential phenotypic elements of clusters in high-dimensional entities

Differential abundance analysis with a right censored covariate in high-dimensional cytometry

Differential Abundant Analysis for Metabolomics, Proteomics and single-cell RNA sequencing Data

Differential cell type change analysis using Logistic/linear Regression

Differential cell-type-specific allelic imbalance

Differential Composition Analysis Transformed by a Similarity matrix

Differential discovery in high-dimensional cytometry via high-resolution clustering

Differential expression analysis and model fitting for single-cell RNA-seq data

Differential expression using kernel-based score test

Differential Gene Expression Analysis for Multi-subject scRNA-seq

Differentially regulated genes from scRNA-seq data

Differential neighbourhood abundance testing on a graph

Differential Topology, Progression and Differentiation.

distinct: a method for differential analyses via hierarchical permutation tests

DtracePLN: Sparse precision matrix estimation via lasso penalized D-trace loss in the multivariate Poisson log-normal model

Dual redundant reference sequencing

Easy single cell analysis platform for enrichment

eSVD2 for performing the eSVD-DE for cohort-wide differential expression analysis

Evaluate Cellspecific Mixing

EWCE for Multiple Gene Lists

Exploratory Analysis of ATAC-seq data

exploratory data analysis of tabula muris droplet counts

Exploring the Human Cell Atlas Data Coordinating Platform

Expression Weighted Celltype Enrichment

Factorial Latent Variable Modeling of Single-Cell RNA-Seq Data

Fast and accurate scRNA-seq cell type identification

Fast and Interpretable Consensus Clustering via Minipatch Learning

Fast Correlation Based Filter for Feature Selection

FCBF-based Co-Expression Networks for Single Cells

FEAture SelcTion (FEAST) for Single-cell clustering

Find breakpoints in Strand-seq data

Fishpond: differential transcript and gene expression with inferential replicates

Fishpond: downstream methods and tools for expression data

Fit a Gamma-Poisson Generalized Linear Model

Flexible, probabilistic metrics for quality control of scRNA-seq data

Functional annotation-driven unsupervised clustering for single-cell data

Functional interpretation of single cell RNA-seq latent manifolds

Functions to conduct quality control analysis in methylation data

Genearting Samples of Gene Expression Data with Variational Autoencoders

Generate Publication Ready Visualizations of Single Cell Transcriptomics Data

Generate QC Reports For Alevin Output

Generating Tree Hierarchy Visualizations from Gene Expression Data

Generation of cell pictures

Gene set analysis accounting for gene-gene correlations

GenoMetric Query Language for R/Bioconductor

Genomic Instability estimation for scRNA-Seq

Genomic trajectories with heterogeneous genetic and environmental backgrounds

HDF5 backend for DelayedArray objects

HDF5 datasets as array-like objects in R

Helper Functions for LIBD Deconvolution

Heterogeneity-Induced Pre-Processing tOol

Hexbin plots for single cell omics data

Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq

Identification and analysis of miRNA sponge regulation

Identify genes associated with multiple expression phenotypes in single-cell CRISPR screening data

Identifying genetic trait/phenotype relevant cell type/state at single cell resolution

Identifying Similar T Cell Receptor Hyper-Variable Sequences with 'ClusTCR2'

Identify Intra and Inter-Donor Variations in Bulk or Single Cell Longitudinal Dataset

ILoReg: a tool for high-resolution cell population identification from scRNA-Seq data

immunoClust - Automated Pipeline for Population Detection in Flow Cytometry

Import methods for 10X Genomics files

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

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

Inferring unobserved perturbations from gene expression data

In-Silico Annotation of Doublets for Single Cell RNA Sequencing Data

Interactive Analysis of Single Cell RNA-Seq Data

Interactive SummarizedExperiment Explorer

Interactive visualization of scRNA-seq data with Cerebro

InterCellar: an R-Shiny app for interactive analysis and exploration of cell-cell communication in single-cell transcriptomics

Interpretable marker-based single-cell pseudotime using Bayesian parametric models

Introduction to Tidy Transcriptomics

IReNA

iSEE Universe

iSMNN: Batch Effect Correction for Single-cell RNA-seq data via Iterative Supervised Mutual Nearest Neighbor Refinement

Iterative Differential Clustering for single-cell

kallisto | bustools R utilities

Label-Free Identification of Endogenous Informative Single Cell Mitochondrial RNA Mutation for Lineage Analysis and Clonal Evolution

Labels normalized cells for CyTOF data and assigns probabilities for each label

Landscape Single Cell Entropy

Large-scale single-cell RNA-seq data manipulation with GDS files

Learn and Apply Cell Type Signatures

Library for (single-cell) SNP array processing

Lineage tracing by indels

Linear model and normality based normalization and transformation method (Linnorm)

Longitudinal Analysis of Cancer Evolution (LACE)

LoomExperiment container

Manipulate Zarr archives as R objects

Mapping, quantification and variant analysis of sequencing data

Marker Enrichment Modeling (MEM)

Mass Spectrometry-Based Single-Cell Proteomics Data Analysis

Merging of phenotype information from different cytometric profiles

Methods for analyzing spatially resolved transcriptomics data

Methods for imaging mass cytometry data analysis

Methods for Single-Cell RNA-Seq Data Analysis

Methods for TCR single-cell embedding

Mine Associated Gene Expressions (from single-cell Rna Seq data)

Mini-batch K-means Clustering for Single-Cell RNA-seq

Minimized Single-Cell Consensus Clustering

Mixture modeling of single-cell RNA-seq data to identify genes with differential distributions

Mixture Nested Effects Models

MLG Clustering

Model-based Analysis of Single Cell Transcriptomics

Model higher-order methylation profiles

Modeling expression drop-out for analysis of scRNA-Seq data

Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-Seq data

Multi-Contrast Gene Set Enrichment Analysis

Multi-function software that performs enrichment, functionally-informed genetic fine-mapping and gene mapping

Multi-Modal Single-Cell Analysis Methods

Multi-sample multi-group scRNA-seq data analysis tools

Multi-Scale Target Explorer

Multiview Intercellular SpaTial modeling framework

Negative binomial model for scRNA-seq

Network smoothing for scRNAseq

NEUral network-based single-Cell Annotation tool

Normalization of Single-Cell mRNA Sequencing Data

Normalization of single cell RNA-seq data

OmniPath web service client and more

ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics

Outlier-aware and Count-based Compositional Analysis of Single-cell Data.

Packaging common Seurat analysis tasks

PCAtools: Everything Principal Components Analysis

PhantomPurgeR

Phenotypic EMD for comparison of single-cell samples

Pipeline for single cell multi-omic data pre-processing

pipeline for single cell RNA-seq data analysis

PLNet: Sparse precision matrix estimation via lasso penalized D-trace loss in the multivariate Poisson log-normal model

PolyA counting and differential transcript usage analysis for scRNA-seq data

Precict cis-co-accessibility from single-cell chromatin accessibility data

Predict cis-co-accessibility from single-cell chromatin accessibility data

Pretrained learning models for cell type prediction on single cell RNA-sequencing data

Rank-based signature enrichment analysis for single-cell data

Rank Constrained Similarity Learning for single cell RNA sequencing data

Rank Constrained Similarity Learning for Single Cell RNA Sequencing Data

R/Bioconductor package to interactively explore and visualize single cell RNA-seq datasets with hierarhical annotations

Reconstruction, visualization and analysis of branching trajectories

Reference-Based Single-Cell RNA-Seq Annotation

Regression Models with Multivariate Outcomes for Mass Cytometry Experiments

Robust Outlier-aware Estimation of Composition and Heterogeneity for Single-cell Data

Run `magic-impute` on scRNA Seq dataset in R

R wrapper for the python openTSNE library

S4 Classes for Single Cell Data

S4 Class for segmented spatial 'omics data

S4 Class for Spatial Experiments handling

S4 Class for Spatially Resolved -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

Scalable Analysis of Differential Transcript Usage for Bulk and Single-Cell RNA-sequencing Applications

Scalable differential expression analysis of single cell transcriptomics datasets with complex study designs

Scalable identification of spatially variable genes in spatially-resolved transcriptomics data

Scaling normalization based on the Pareto distribution

scClassify: single-cell Hierarchical Classification

scDataviz: single cell dataviz and downstream analyses

scDblFinder

SCENIC (Single Cell rEgulatory Network Inference and Clustering)

scFeatures: Multi-view representations of single-cell and spatial data for disease outcome prediction

sciCNV

Scifer: Single-Cell Immunoglobulin Filtering of Sanger Sequences

scMerge: Merging multiple batches of scRNA-seq data

scraps output import and processing in R

scReClassify: post hoc cell type classification 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

ScRNA-seq Workflow CONCLUS - From CONsensus CLUSters To A Meaningful CONCLUSion

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

Simplify production of computable OSCA texts and artifacts for AnVIL

Simulate Bulk RNA-seq Datasets from Single-Cell Datasets

Simulation and Deconvolution of Omic Profiles

Simulation, power evaluation, and sample size recommendation for single cell RNA-seq

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 Batch Correction Methods

Single-Cell Consensus Clustering

Single-Cell Data Visualisation Using Kernel Gene-Weighted Density Estimation

Single cell differential composition analysis

Single Cell Entropy

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 Pipeline

Single cell replicability analysis

Single-Cell RNA-Seq Analysis Utilities

Single-cell RNAseq cell cluster labelling by reference

Single-cell RNA-seq toolkit

Single-cell RNA sequencing data normalization

Single Cell RNA-Seq UMI Filtering Facilitator (scruff)

Single-Cell RNA-Seq Utilities

Single Cell Shiny Application for Analysing Single Cell Transcriptomics Data

Single-Cell Trajectory Analysis Utilities

Single-Cell UTR Bootstrap Tools

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

spatialHeatmap

Spatial Image Analysis of Tissues

Spatial Reconstruction of Tissues from scRNA-seq Data

Spatial transcriptomic clustering

Spatial Transcriptomics Analysis

SpotClean adjusts for spot swapping in spatial transcriptomics data

`SPOTlight`: Spatial Transcriptomics Deconvolution

Stabilised mosaic single cell data integration using unshared features

Standardize Antibody Names

Stan implementation of BASiCS

Statistical Inferences with MeDIP-seq Data (SIMD) to infer the methylation level for each CpG site

Statistical methods for analysing single cell RNA-seq data

Statistical tests for detecting differential distributions based on the 2-Wasserstein distance

Structure Learning for Count Data

Survival of patients using ors on TCGA data

Switch-like differential expression across single-cell trajectories

Targeted scRNA-seq primer design for TAP-seq

The scigenex package (Single-Cell Informative GENe Explorer)

The slim version of signac

This Package Discovers Directionality in Time and Pseudo-times Series of Gene Expression Patterns

Tidy Transcriptomics for Single-cell RNA Sequencing Analyses

Toolkit for Single-Cell Velocity

Tools for Assessing Clustering

Tools for finding Total RNA Expression Genes in single nucleus RNA-seq data

Tools for matrices with precision weights, test and explore weighted or sparse data

Tools for ordering single-cell sequencing

Tools for processing of high-dimensional cytometry data

trajectory-based differential expression analysis for sequencing data

Trajectory functions for visualization and interpretation.

Transcript Quantification Import with Automatic Metadata

Tree Aggregation

tricycle: Transferable Representation and Inference of cell cycle

TRONCO, an R package for TRanslational ONCOlogy

Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

Unbiased Extraction of Single Cell Identity using Multiple Correspondence Analysis

User Friendly Single-Cell and Bulk RNA Sequencing Visualization

Using Mass Cytometry for Differential Abundance Analyses

Utilities for Handling Single-Cell Droplet Data

Variance Stabilizing Transformation for Gamma-Poisson Models

Varying-Censoring Aware Matrix Factorization

Visualization functions for spatial transcriptomics data

Visualization of highly multiplexed imaging data in R

Visualization of Methylation Data

What the Package Does (One Line, Title Case)

What the Package Does TODOELI

Wind: weighted indexes for clustering evaluation

Yet Another Single-Cell Analysis Toolkit (Yeskit)

Zero-Inflated Negative Binomial Model for RNA-Seq Data

Biocview "SingleCell"

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