R-universe search: needs:RcppAnnoy

satijalab

Seurat:Tools for Single Cell Genomics

A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.

Maintained by Paul Hoffman. Last updated 1 years ago.

human-cell-atlas single-cell-genomics single-cell-rna-seq cpp

2.4k stars 16.86 score 50k scripts 73 dependents

jlmelville

uwot:The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction

An implementation of the Uniform Manifold Approximation and Projection dimensionality reduction by McInnes et al. (2018) <doi:10.48550/arXiv.1802.03426>. It also provides means to transform new data and to carry out supervised dimensionality reduction. An implementation of the related LargeVis method of Tang et al. (2016) <doi:10.48550/arXiv.1602.00370> is also provided. This is a complete re-implementation in R (and C++, via the 'Rcpp' package): no Python installation is required. See the uwot website (<https://github.com/jlmelville/uwot>) for more documentation and examples.

Maintained by James Melville. Last updated 2 days ago.

dimensionality-reduction umap cpp

329 stars 16.08 score 2.0k scripts 145 dependents

bioc

scDblFinder:scDblFinder

The scDblFinder package gathers various methods for the detection and handling of doublets/multiplets in single-cell sequencing data (i.e. multiple cells captured within the same droplet or reaction volume). It includes methods formerly found in the scran package, the new fast and comprehensive scDblFinder method, and a reimplementation of the Amulet detection method for single-cell ATAC-seq.

Maintained by Pierre-Luc Germain. Last updated 8 days ago.

preprocessing singlecell rnaseq atacseq doublets single-cell

184 stars 12.38 score 888 scripts 1 dependents

bioc

mia:Microbiome analysis

mia implements tools for microbiome analysis based on the SummarizedExperiment, SingleCellExperiment and TreeSummarizedExperiment infrastructure. Data wrangling and analysis in the context of taxonomic data is the main scope. Additional functions for common task are implemented such as community indices calculation and summarization.

Maintained by Tuomas Borman. Last updated 14 days ago.

microbiome software dataimport analysis bioconductor

52 stars 11.50 score 316 scripts 5 dependents

bioc

scater:Single-Cell Analysis Toolkit for Gene Expression Data in R

A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control and visualization.

Maintained by Alan OCallaghan. Last updated 21 days ago.

immunooncology singlecell rnaseq qualitycontrol preprocessing normalization visualization dimensionreduction transcriptomics geneexpression sequencing software dataimport datarepresentation infrastructure coverage

11.07 score 12k scripts 43 dependents

bioc

CATALYST:Cytometry dATa anALYSis Tools

CATALYST provides tools for preprocessing of and differential discovery in cytometry data such as FACS, CyTOF, and IMC. Preprocessing includes i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation. For differential discovery, the package provides a number of convenient functions for data processing (e.g., clustering, dimension reduction), as well as a suite of visualizations for exploratory data analysis and exploration of results from differential abundance (DA) and state (DS) analysis in order to identify differences in composition and expression profiles at the subpopulation-level, respectively.

Maintained by Helena L. Crowell. Last updated 4 months ago.

clustering dataimport differentialexpression experimentaldesign flowcytometry immunooncology massspectrometry normalization preprocessing singlecell software statisticalmethod visualization

67 stars 11.06 score 362 scripts 2 dependents

bioc

infercnv:Infer Copy Number Variation from Single-Cell RNA-Seq Data

Using single-cell RNA-Seq expression to visualize CNV in cells.

Maintained by Christophe Georgescu. Last updated 5 months ago.

software copynumbervariation variantdetection structuralvariation genomicvariation genetics transcriptomics statisticalmethod bayesian hiddenmarkovmodel singlecell jags cpp

601 stars 10.92 score 674 scripts

welch-lab

rliger:Linked Inference of Genomic Experimental Relationships

Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) <doi:10.1016/j.cell.2019.05.006>, and Liu J, Gao C, Sodicoff J, et al (2020) <doi:10.1038/s41596-020-0391-8> for more details.

Maintained by Yichen Wang. Last updated 2 months ago.

nonnegative-matrix-factorization single-cell openblas cpp

408 stars 10.77 score 334 scripts 1 dependents

bioc

celda:CEllular Latent Dirichlet Allocation

Celda is a suite of Bayesian hierarchical models for clustering single-cell RNA-sequencing (scRNA-seq) data. It is able to perform "bi-clustering" and simultaneously cluster genes into gene modules and cells into cell subpopulations. It also contains DecontX, a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. A variety of scRNA-seq data visualization functions is also included.

Maintained by Joshua Campbell. Last updated 1 months ago.

singlecell geneexpression clustering sequencing bayesian immunooncology dataimport cpp openmp

147 stars 10.47 score 256 scripts 2 dependents

bioc

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

`muscat` provides various methods and visualization tools for DS analysis in multi-sample, multi-group, multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and methods based on aggregated “pseudobulk” data, as well as a flexible simulation platform that mimics both single and multi-sample scRNA-seq data.

Maintained by Helena L. Crowell. Last updated 5 months ago.

immunooncology differentialexpression sequencing singlecell software statisticalmethod visualization

181 stars 10.26 score 686 scripts

bioc

singleCellTK:Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

The Single Cell Toolkit (SCTK) in the singleCellTK package provides an interface to popular tools for importing, quality control, analysis, and visualization of single cell RNA-seq data. SCTK allows users to seamlessly integrate tools from various packages at different stages of the analysis workflow. A general "a la carte" workflow gives users the ability access to multiple methods for data importing, calculation of general QC metrics, doublet detection, ambient RNA estimation and removal, filtering, normalization, batch correction or integration, dimensionality reduction, 2-D embedding, clustering, marker detection, differential expression, cell type labeling, pathway analysis, and data exporting. Curated workflows can be used to run Seurat and Celda. Streamlined quality control can be performed on the command line using the SCTK-QC pipeline. Users can analyze their data using commands in the R console or by using an interactive Shiny Graphical User Interface (GUI). Specific analyses or entire workflows can be summarized and shared with comprehensive HTML reports generated by Rmarkdown. Additional documentation and vignettes can be found at camplab.net/sctk.

Maintained by Joshua David Campbell. Last updated 1 months ago.

singlecell geneexpression differentialexpression alignment clustering immunooncology batcheffect normalization qualitycontrol dataimport gui

182 stars 10.17 score 252 scripts

constantamateur

SoupX:Single Cell mRNA Soup eXterminator

Quantify, profile and remove ambient mRNA contamination (the "soup") from droplet based single cell RNA-seq experiments. Implements the method described in Young et al. (2018) <doi:10.1101/303727>.

Maintained by Matthew Daniel Young. Last updated 2 years ago.

266 stars 10.08 score 594 scripts 1 dependents

bioc

MOFA2:Multi-Omics Factor Analysis v2

The MOFA2 package contains a collection of tools for training and analysing multi-omic factor analysis (MOFA). MOFA is a probabilistic factor model that aims to identify principal axes of variation from data sets that can comprise multiple omic layers and/or groups of samples. Additional time or space information on the samples can be incorporated using the MEFISTO framework, which is part of MOFA2. Downstream analysis functions to inspect molecular features underlying each factor, vizualisation, imputation etc are available.

Maintained by Ricard Argelaguet. Last updated 5 months ago.

dimensionreduction bayesian visualization factor-analysis mofa multi-omics

319 stars 10.02 score 502 scripts

bioc

scMerge:scMerge: Merging multiple batches of scRNA-seq data

Like all gene expression data, single-cell data suffers from batch effects and other unwanted variations that makes accurate biological interpretations difficult. The scMerge method leverages factor analysis, stably expressed genes (SEGs) and (pseudo-) replicates to remove unwanted variations and merge multiple single-cell data. This package contains all the necessary functions in the scMerge pipeline, including the identification of SEGs, replication-identification methods, and merging of single-cell data.

Maintained by Yingxin Lin. Last updated 5 months ago.

batcheffect geneexpression normalization rnaseq sequencing singlecell software transcriptomics bioinformatics single-cell

67 stars 9.52 score 137 scripts 1 dependents

stemangiola

tidyseurat:Brings Seurat to the Tidyverse

It creates an invisible layer that allow to see the 'Seurat' object as tibble and interact seamlessly with the tidyverse.

Maintained by Stefano Mangiola. Last updated 8 months ago.

assaydomain infrastructure rnaseq differentialexpression geneexpression normalization clustering qualitycontrol sequencing transcription transcriptomics dplyr ggplot2 pca purrr sct seurat single-cell single-cell-rna-seq tibble tidyr tidyverse transcripts tsne umap

159 stars 9.48 score 398 scripts 1 dependents

tidymodels

embed:Extra Recipes for Encoding Predictors

Predictors can be converted to one or more numeric representations using a variety of methods. Effect encodings using simple generalized linear models <doi:10.48550/arXiv.1611.09477> or nonlinear models <doi:10.48550/arXiv.1604.06737> can be used. There are also functions for dimension reduction and other approaches.

Maintained by Emil Hvitfeldt. Last updated 2 months ago.

142 stars 9.35 score 1.1k scripts

bioc

Banksy:Spatial transcriptomic clustering

Banksy is an R package that incorporates spatial information to cluster cells in a feature space (e.g. gene expression). To incorporate spatial information, BANKSY computes the mean neighborhood expression and azimuthal Gabor filters that capture gene expression gradients. These features are combined with the cell's own expression to embed cells in a neighbor-augmented product space which can then be clustered, allowing for accurate and spatially-aware cell typing and tissue domain segmentation.

Maintained by Joseph Lee. Last updated 24 days ago.

clustering spatial singlecell geneexpression dimensionreduction clustering-algorithm single-cell-omics spatial-omics

90 stars 9.03 score 248 scripts

bioc

BayesSpace:Clustering and Resolution Enhancement of Spatial Transcriptomes

Tools for clustering and enhancing the resolution of spatial gene expression experiments. BayesSpace clusters a low-dimensional representation of the gene expression matrix, incorporating a spatial prior to encourage neighboring spots to cluster together. The method can enhance the resolution of the low-dimensional representation into "sub-spots", for which features such as gene expression or cell type composition can be imputed.

Maintained by Matt Stone. Last updated 5 months ago.

software clustering transcriptomics geneexpression singlecell immunooncology dataimport openblas cpp openmp

123 stars 8.89 score 278 scripts 1 dependents

bioc

miaViz:Microbiome Analysis Plotting and Visualization

The miaViz package implements functions to visualize TreeSummarizedExperiment objects especially in the context of microbiome analysis. Part of the mia family of R/Bioconductor packages.

Maintained by Tuomas Borman. Last updated 9 days ago.

microbiome software visualization bioconductor microbiome-analysis plotting

10 stars 8.67 score 81 scripts 1 dependents

bioc

M3Drop:Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

This package fits a model to the pattern of dropouts in single-cell RNASeq data. This model is used as a null to identify significantly variable (i.e. differentially expressed) genes for use in downstream analysis, such as clustering cells. Also includes an method for calculating exact Pearson residuals in UMI-tagged data using a library-size aware negative binomial model.

Maintained by Tallulah Andrews. Last updated 5 months ago.

rnaseq sequencing transcriptomics geneexpression software differentialexpression dimensionreduction featureextraction human-cell-atlas rna-seq single-cell single-cell-rna-seq

29 stars 8.53 score 119 scripts 2 dependents

bioc

SIMLR:Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)

Single-cell RNA-seq technologies enable high throughput gene expression measurement of individual cells, and allow the discovery of heterogeneity within cell populations. Measurement of cell-to-cell gene expression similarity is critical for the identification, visualization and analysis of cell populations. However, single-cell data introduce challenges to conventional measures of gene expression similarity because of the high level of noise, outliers and dropouts. We develop a novel similarity-learning framework, SIMLR (Single-cell Interpretation via Multi-kernel LeaRning), which learns an appropriate distance metric from the data for dimension reduction, clustering and visualization.

Maintained by Luca De Sano. Last updated 3 days ago.

immunooncology clustering geneexpression sequencing singlecell openblas cpp

110 stars 8.48 score 69 scripts

samuel-marsh

scCustomize:Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

Collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using 'R'. 'scCustomize' aims to provide 1) Customized visualizations for aid in ease of use and to create more aesthetic and functional visuals. 2) Improve speed/reproducibility of common tasks/pieces of code in scRNA-seq analysis with a single or group of functions. For citation please use: Marsh SE (2021) "Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing" <doi:10.5281/zenodo.5706430> RRID:SCR_024675.

Maintained by Samuel Marsh. Last updated 3 months ago.

customization ggplot2 scrna-seq seurat single-cell single-cell-genomics single-cell-rna-seq visualization

246 stars 8.45 score 1.1k scripts

bioc

lefser:R implementation of the LEfSE method for microbiome biomarker discovery

lefser is the R implementation of the popular microbiome biomarker discovery too, LEfSe. It uses the Kruskal-Wallis test, Wilcoxon-Rank Sum test, and Linear Discriminant Analysis to find biomarkers from two-level classes (and optional sub-classes).

Maintained by Sehyun Oh. Last updated 1 months ago.

software sequencing differentialexpression microbiome statisticalmethod classification bioconductor-package r01ca230551

56 stars 8.44 score 56 scripts

carmonalab

scGate:Marker-Based Cell Type Purification for Single-Cell Sequencing Data

A common bioinformatics task in single-cell data analysis is to purify a cell type or cell population of interest from heterogeneous datasets. 'scGate' automatizes marker-based purification of specific cell populations, without requiring training data or reference gene expression profiles. Briefly, 'scGate' takes as input: i) a gene expression matrix stored in a 'Seurat' object and ii) a “gating model” (GM), consisting of a set of marker genes that define the cell population of interest. The GM can be as simple as a single marker gene, or a combination of positive and negative markers. More complex GMs can be constructed in a hierarchical fashion, akin to gating strategies employed in flow cytometry. 'scGate' evaluates the strength of signature marker expression in each cell using the rank-based method 'UCell', and then performs k-nearest neighbor (kNN) smoothing by calculating the mean 'UCell' score across neighboring cells. kNN-smoothing aims at compensating for the large degree of sparsity in scRNA-seq data. Finally, a universal threshold over kNN-smoothed signature scores is applied in binary decision trees generated from the user-provided gating model, to annotate cells as either “pure” or “impure”, with respect to the cell population of interest. See the related publication Andreatta et al. (2022) <doi:10.1093/bioinformatics/btac141>.

Maintained by Massimo Andreatta. Last updated 2 months ago.

filtering marker-genes scgate signatures single-cell

106 stars 8.38 score 163 scripts

stephenslab

fastTopics:Fast Algorithms for Fitting Topic Models and Non-Negative Matrix Factorizations to Count Data

Implements fast, scalable optimization algorithms for fitting topic models ("grade of membership" models) and non-negative matrix factorizations to count data. The methods exploit the special relationship between the multinomial topic model (also, "probabilistic latent semantic indexing") and Poisson non-negative matrix factorization. The package provides tools to compare, annotate and visualize model fits, including functions to efficiently create "structure plots" and identify key features in topics. The 'fastTopics' package is a successor to the 'CountClust' package. For more information, see <doi:10.48550/arXiv.2105.13440> and <doi:10.1186/s13059-023-03067-9>. Please also see the GitHub repository for additional vignettes not included in the package on CRAN.

Maintained by Peter Carbonetto. Last updated 29 days ago.

openblas cpp

79 stars 8.38 score 678 scripts 1 dependents

willwerscheid

flashier:Empirical Bayes Matrix Factorization

Methods for matrix factorization based on Wang and Stephens (2021) <https://jmlr.org/papers/v22/20-589.html>.

Maintained by Jason Willwerscheid. Last updated 2 months ago.

11 stars 8.32 score 266 scripts

bioc

POMA:Tools for Omics Data Analysis

The POMA package offers a comprehensive toolkit designed for omics data analysis, streamlining the process from initial visualization to final statistical analysis. Its primary goal is to simplify and unify the various steps involved in omics data processing, making it more accessible and manageable within a single, intuitive R package. Emphasizing on reproducibility and user-friendliness, POMA leverages the standardized SummarizedExperiment class from Bioconductor, ensuring seamless integration and compatibility with a wide array of Bioconductor tools. This approach guarantees maximum flexibility and replicability, making POMA an essential asset for researchers handling omics datasets. See https://github.com/pcastellanoescuder/POMAShiny. Paper: Castellano-Escuder et al. (2021) <doi:10.1371/journal.pcbi.1009148> for more details.

Maintained by Pol Castellano-Escuder. Last updated 4 months ago.

batcheffect classification clustering decisiontree dimensionreduction multidimensionalscaling normalization preprocessing principalcomponent regression rnaseq software statisticalmethod visualization bioconductor bioinformatics data-visualization dimension-reduction exploratory-data-analysis machine-learning omics-data-integration pipeline pre-processing statistical-analysis user-friendly workflow

11 stars 8.16 score 20 scripts 1 dependents

kharchenkolab

pagoda2:Single Cell Analysis and Differential Expression

Analyzing and interactively exploring large-scale single-cell RNA-seq datasets. 'pagoda2' primarily performs normalization and differential gene expression analysis, with an interactive application for exploring single-cell RNA-seq datasets. It performs basic tasks such as cell size normalization, gene variance normalization, and can be used to identify subpopulations and run differential expression within individual samples. 'pagoda2' was written to rapidly process modern large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application allows users to explore which gene expression patterns form the different subpopulations within your data. The package also serves as the primary method for preprocessing data for conos, <https://github.com/kharchenkolab/conos>. This package interacts with data available through the 'p2data' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/pagoda2>. The size of the 'p2data' package is approximately 6 MB.

Maintained by Evan Biederstedt. Last updated 1 years ago.

scrna-seq single-cell single-cell-rna-seq transcriptomics openblas cpp openmp

223 stars 8.00 score 282 scripts

bioc

FLAMES:FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data

Semi-supervised isoform detection and annotation from both bulk and single-cell long read RNA-seq data. Flames provides automated pipelines for analysing isoforms, as well as intermediate functions for manual execution.

Maintained by Changqing Wang. Last updated 18 days ago.

rnaseq singlecell transcriptomics dataimport differentialsplicing alternativesplicing geneexpression longread zlib curl bzip2 xz-utils cpp

31 stars 7.95 score 12 scripts

bioc

COTAN:COexpression Tables ANalysis

Statistical and computational method to analyze the co-expression of gene pairs at single cell level. It provides the foundation for single-cell gene interactome analysis. The basic idea is studying the zero UMI counts' distribution instead of focusing on positive counts; this is done with a generalized contingency tables framework. COTAN can effectively assess the correlated or anti-correlated expression of gene pairs. It provides a numerical index related to the correlation and an approximate p-value for the associated independence test. COTAN can also evaluate whether single genes are differentially expressed, scoring them with a newly defined global differentiation index. Moreover, this approach provides ways to plot and cluster genes according to their co-expression pattern with other genes, effectively helping the study of gene interactions and becoming a new tool to identify cell-identity marker genes.

Maintained by Galfrè Silvia Giulia. Last updated 1 months ago.

systemsbiology transcriptomics geneexpression singlecell

16 stars 7.85 score 96 scripts

bioc

MGnifyR:R interface to EBI MGnify metagenomics resource

Utility package to facilitate integration and analysis of EBI MGnify data in R. The package can be used to import microbial data for instance into TreeSummarizedExperiment (TreeSE). In TreeSE format, the data is directly compatible with miaverse framework.

Maintained by Tuomas Borman. Last updated 5 months ago.

infrastructure dataimport metagenomics

21 stars 7.61 score 32 scripts

bioc

ggsc:Visualizing Single Cell and Spatial Transcriptomics

Useful functions to visualize single cell and spatial data. It supports visualizing 'Seurat', 'SingleCellExperiment' and 'SpatialExperiment' objects through grammar of graphics syntax implemented in 'ggplot2'.

Maintained by Guangchuang Yu. Last updated 5 months ago.

dimensionreduction geneexpression singlecell software spatial transcriptomics visualization openblas cpp openmp

47 stars 7.59 score 18 scripts

bioc

MOSim:Multi-Omics Simulation (MOSim)

MOSim package simulates multi-omic experiments that mimic regulatory mechanisms within the cell, allowing flexible experimental design including time course and multiple groups.

Maintained by Sonia Tarazona. Last updated 5 months ago.

software timecourse experimentaldesign rnaseq cpp

9 stars 7.46 score 11 scripts

bioc

netSmooth:Network smoothing for scRNAseq

netSmooth is an R package for network smoothing of single cell RNA sequencing data. Using bio networks such as protein-protein interactions as priors for gene co-expression, netsmooth improves cell type identification from noisy, sparse scRNAseq data.

Maintained by Jonathan Ronen. Last updated 5 months ago.

network graphandnetwork singlecell rnaseq geneexpression sequencing transcriptomics normalization preprocessing clustering dimensionreduction bioinformatics genomics single-cell

27 stars 7.41 score 4 scripts

kharchenkolab

conos:Clustering on Network of Samples

Wires together large collections of single-cell RNA-seq datasets, which allows for both the identification of recurrent cell clusters and the propagation of information between datasets in multi-sample or atlas-scale collections. 'Conos' focuses on the uniform mapping of homologous cell types across heterogeneous sample collections. For instance, users could investigate a collection of dozens of peripheral blood samples from cancer patients combined with dozens of controls, which perhaps includes samples of a related tissue such as lymph nodes. This package interacts with data available through the 'conosPanel' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/conos>. The size of the 'conosPanel' package is approximately 12 MB.

Maintained by Evan Biederstedt. Last updated 1 years ago.

batch-correction scrna-seq single-cell-rna-seq openblas cpp openmp

205 stars 7.33 score 258 scripts

bioc

CuratedAtlasQueryR:Queries the Human Cell Atlas

Provides access to a copy of the Human Cell Atlas, but with harmonised metadata. This allows for uniform querying across numerous datasets within the Atlas using common fields such as cell type, tissue type, and patient ethnicity. Usage involves first querying the metadata table for cells of interest, and then downloading the corresponding cells into a SingleCellExperiment object.

Maintained by Stefano Mangiola. Last updated 5 months ago.

assaydomain infrastructure rnaseq differentialexpression geneexpression normalization clustering qualitycontrol sequencing transcription transcriptomics database duckdb hdf5 human-cell-atlas single-cell singlecellexperiment tidyverse

90 stars 7.04 score 41 scripts

bioc

pipeComp:pipeComp pipeline benchmarking framework

A simple framework to facilitate the comparison of pipelines involving various steps and parameters. The `pipelineDefinition` class represents pipelines as, minimally, a set of functions consecutively executed on the output of the previous one, and optionally accompanied by step-wise evaluation and aggregation functions. Given such an object, a set of alternative parameters/methods, and benchmark datasets, the `runPipeline` function then proceeds through all combinations arguments, avoiding recomputing the same step twice and compiling evaluations on the fly to avoid storing potentially large intermediate data.

Maintained by Pierre-Luc Germain. Last updated 5 months ago.

geneexpression transcriptomics clustering datarepresentation benchmark bioconductor pipeline-benchmarking pipelines single-cell-rna-seq

41 stars 7.02 score 43 scripts

bioc

musicatk:Mutational Signature Comprehensive Analysis Toolkit

Mutational signatures are carcinogenic exposures or aberrant cellular processes that can cause alterations to the genome. We created musicatk (MUtational SIgnature Comprehensive Analysis ToolKit) to address shortcomings in versatility and ease of use in other pre-existing computational tools. Although many different types of mutational data have been generated, current software packages do not have a flexible framework to allow users to mix and match different types of mutations in the mutational signature inference process. Musicatk enables users to count and combine multiple mutation types, including SBS, DBS, and indels. Musicatk calculates replication strand, transcription strand and combinations of these features along with discovery from unique and proprietary genomic feature associated with any mutation type. Musicatk also implements several methods for discovery of new signatures as well as methods to infer exposure given an existing set of signatures. Musicatk provides functions for visualization and downstream exploratory analysis including the ability to compare signatures between cohorts and find matching signatures in COSMIC V2 or COSMIC V3.

Maintained by Joshua D. Campbell. Last updated 5 months ago.

software biologicalquestion somaticmutation variantannotation

13 stars 6.97 score 20 scripts

bioc

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

The package comprises a set of pretrained machine learning models to predict basic immune cell types. This enables all users to quickly get a first annotation of the cell types present in their dataset without requiring prior knowledge. scAnnotatR also allows users to train their own models to predict new cell types based on specific research needs.

Maintained by Johannes Griss. Last updated 5 months ago.

singlecell transcriptomics geneexpression supportvectormachine classification software

15 stars 6.61 score 20 scripts

bioc

CiteFuse:CiteFuse: multi-modal analysis of CITE-seq data

CiteFuse pacakage implements a suite of methods and tools for CITE-seq data from pre-processing to integrative analytics, including doublet detection, network-based modality integration, cell type clustering, differential RNA and protein expression analysis, ADT evaluation, ligand-receptor interaction analysis, and interactive web-based visualisation of the analyses.

Maintained by Yingxin Lin. Last updated 5 months ago.

singlecell geneexpression bioinformatics single-cell cpp

27 stars 6.59 score 18 scripts

carmonalab

GeneNMF:Non-Negative Matrix Factorization for Single-Cell Omics

A collection of methods to extract gene programs from single-cell gene expression data using non-negative matrix factorization (NMF). 'GeneNMF' contains functions to directly interact with the 'Seurat' toolkit and derive interpretable gene program signatures.

Maintained by Massimo Andreatta. Last updated 10 days ago.

105 stars 6.58 score 12 scripts

bioc

tricycle:tricycle: Transferable Representation and Inference of cell cycle

The package contains functions to infer and visualize cell cycle process using Single Cell RNASeq data. It exploits the idea of transfer learning, projecting new data to the previous learned biologically interpretable space. We provide a pre-learned cell cycle space, which could be used to infer cell cycle time of human and mouse single cell samples. In addition, we also offer functions to visualize cell cycle time on different embeddings and functions to build new reference.

Maintained by Shijie Zheng. Last updated 5 months ago.

singlecell software transcriptomics rnaseq transcription biologicalquestion dimensionreduction immunooncology

25 stars 6.54 score 46 scripts

bioc

SpotClean:SpotClean adjusts for spot swapping in spatial transcriptomics data

SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data. Recent spatial transcriptomics experiments utilize slides containing thousands of spots with spot-specific barcodes that bind mRNA. Ideally, unique molecular identifiers at a spot measure spot-specific expression, but this is often not the case due to bleed from nearby spots, an artifact we refer to as spot swapping. SpotClean is able to estimate the contamination rate in observed data and decontaminate the spot swapping effect, thus increase the sensitivity and precision of downstream analyses.

Maintained by Zijian Ni. Last updated 5 months ago.

dataimport rnaseq sequencing geneexpression spatial singlecell transcriptomics preprocessing rna-seq spatial-transcriptomics

31 stars 6.52 score 36 scripts

bioc

condiments:Differential Topology, Progression and Differentiation

This package encapsulate many functions to conduct a differential topology analysis. It focuses on analyzing an 'omic dataset with multiple conditions. While the package is mostly geared toward scRNASeq, it does not place any restriction on the actual input format.

Maintained by Hector Roux de Bezieux. Last updated 4 months ago.

rnaseq sequencing software singlecell transcriptomics multiplecomparison visualization

26 stars 6.52 score 17 scripts

bioc

CatsCradle:This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters

This package addresses two broad areas. It allows for in-depth analysis of spatial transcriptomic data by identifying tissue neighbourhoods. These are contiguous regions of tissue surrounding individual cells. 'CatsCradle' allows for the categorisation of neighbourhoods by the cell types contained in them and the genes expressed in them. In particular, it produces Seurat objects whose individual elements are neighbourhoods rather than cells. In addition, it enables the categorisation and annotation of genes by producing Seurat objects whose elements are genes.

Maintained by Michael Shapiro. Last updated 11 days ago.

biologicalquestion statisticalmethod geneexpression singlecell transcriptomics spatial

3 stars 6.52 score

kharchenkolab

sccore:Core Utilities for Single-Cell RNA-Seq

Core utilities for single-cell RNA-seq data analysis. Contained within are utility functions for working with differential expression (DE) matrices and count matrices, a collection of functions for manipulating and plotting data via 'ggplot2', and functions to work with cell graphs and cell embeddings. Graph-based methods include embedding kNN cell graphs into a UMAP <doi:10.21105/joss.00861>, collapsing vertices of each cluster in the graph, and propagating graph labels.

Maintained by Evan Biederstedt. Last updated 1 years ago.

cpp

12 stars 6.46 score 36 scripts 9 dependents

mathewchamberlain

SignacX:Cell Type Identification and Discovery from Single Cell Gene Expression Data

An implementation of neural networks trained with flow-sorted gene expression data to classify cellular phenotypes in single cell RNA-sequencing data. See Chamberlain M et al. (2021) <doi:10.1101/2021.02.01.429207> for more details.

Maintained by Mathew Chamberlain. Last updated 2 years ago.

cellular-phenotypes seurat single-cell-rna-seq

24 stars 6.46 score 34 scripts

qile0317

APackOfTheClones:Visualization of Clonal Expansion for Single Cell Immune Profiles

Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles. The method was originally implemented by Murray Christian and Ben Murrell in the following immunology study: Ma et al. (2021) <doi:10.1126/sciimmunol.abg6356>.

Maintained by Qile Yang. Last updated 4 months ago.

clonal-analysis immune-repertoire immune-system scrna-seq scrnaseq seurat single-cell single-cell-genomics cpp

15 stars 6.45 score 15 scripts

lhe17

nebula:Negative Binomial Mixed Models Using Large-Sample Approximation for Differential Expression Analysis of ScRNA-Seq Data

A fast negative binomial mixed model for conducting association analysis of multi-subject single-cell data. It can be used for identifying marker genes, differential expression and co-expression analyses. The model includes subject-level random effects to account for the hierarchical structure in multi-subject single-cell data. See He et al. (2021) <doi:10.1038/s42003-021-02146-6>.

Maintained by Liang He. Last updated 3 days ago.

cpp

37 stars 6.43 score 145 scripts

duct317

scDHA:Single-Cell Decomposition using Hierarchical Autoencoder

Provides a fast and accurate pipeline for single-cell analyses. The 'scDHA' software package can perform clustering, dimension reduction and visualization, classification, and time-trajectory inference on single-cell data (Tran et.al. (2021) <DOI:10.1038/s41467-021-21312-2>).

Maintained by Ha Nguyen. Last updated 12 months ago.

cpp

40 stars 6.38 score 20 scripts 2 dependents

bioc

distinct:distinct: a method for differential analyses via hierarchical permutation tests

distinct is a statistical method to perform differential testing between two or more groups of distributions; differential testing is performed via hierarchical non-parametric permutation tests on the cumulative distribution functions (cdfs) of each sample. While most methods for differential expression target differences in the mean abundance between conditions, distinct, by comparing full cdfs, identifies, both, differential patterns involving changes in the mean, as well as more subtle variations that do not involve the mean (e.g., unimodal vs. bi-modal distributions with the same mean). distinct is a general and flexible tool: due to its fully non-parametric nature, which makes no assumptions on how the data was generated, it can be applied to a variety of datasets. It is particularly suitable to perform differential state analyses on single cell data (i.e., differential analyses within sub-populations of cells), such as single cell RNA sequencing (scRNA-seq) and high-dimensional flow or mass cytometry (HDCyto) data. To use distinct one needs data from two or more groups of samples (i.e., experimental conditions), with at least 2 samples (i.e., biological replicates) per group.

Maintained by Simone Tiberi. Last updated 5 months ago.

genetics rnaseq sequencing differentialexpression geneexpression multiplecomparison software transcription statisticalmethod visualization singlecell flowcytometry genetarget openblas cpp

11 stars 6.35 score 34 scripts 1 dependents

bioc

CellMixS:Evaluate Cellspecific Mixing

CellMixS provides metrics and functions to evaluate batch effects, data integration and batch effect correction in single cell trancriptome data with single cell resolution. Results can be visualized and summarised on different levels, e.g. on cell, celltype or dataset level.

Maintained by Almut Lütge. Last updated 5 months ago.

singlecell transcriptomics geneexpression batcheffect

7 stars 6.35 score 64 scripts

bioc

scDataviz:scDataviz: single cell dataviz and downstream analyses

In the single cell World, which includes flow cytometry, mass cytometry, single-cell RNA-seq (scRNA-seq), and others, there is a need to improve data visualisation and to bring analysis capabilities to researchers even from non-technical backgrounds. scDataviz attempts to fit into this space, while also catering for advanced users. Additonally, due to the way that scDataviz is designed, which is based on SingleCellExperiment, it has a 'plug and play' feel, and immediately lends itself as flexibile and compatibile with studies that go beyond scDataviz. Finally, the graphics in scDataviz are generated via the ggplot engine, which means that users can 'add on' features to these with ease.

Maintained by Kevin Blighe. Last updated 5 months ago.

singlecell immunooncology rnaseq geneexpression transcription flowcytometry massspectrometry dataimport

63 stars 6.30 score 16 scripts

bioc

iSEEtree:Interactive visualisation for microbiome data

iSEEtree is an extension of iSEE for the TreeSummarizedExperiment data container. It provides interactive panel designs to explore hierarchical datasets, such as the microbiome and cell lines.

Maintained by Giulio Benedetti. Last updated 9 days ago.

software visualization microbiome gui shinyapps dataimport shiny-apps visualisation

3 stars 6.28 score 5 scripts

feiyoung

DR.SC:Joint Dimension Reduction and Spatial Clustering

Joint dimension reduction and spatial clustering is conducted for Single-cell RNA sequencing and spatial transcriptomics data, and more details can be referred to Wei Liu, Xu Liao, Yi Yang, Huazhen Lin, Joe Yeong, Xiang Zhou, Xingjie Shi and Jin Liu. (2022) <doi:10.1093/nar/gkac219>. It is not only computationally efficient and scalable to the sample size increment, but also is capable of choosing the smoothness parameter and the number of clusters as well.

Maintained by Wei Liu. Last updated 1 years ago.

dimension-reduction selfsupervised spatial-clustering spatial-transcriptomics openblas cpp

5 stars 6.12 score 29 scripts 2 dependents

bioc

tidyomics:Easily install and load the tidyomics ecosystem

The tidyomics ecosystem is a set of packages for ’omic data analysis that work together in harmony; they share common data representations and API design, consistent with the tidyverse ecosystem. The tidyomics package is designed to make it easy to install and load core packages from the tidyomics ecosystem with a single command.

Maintained by Stefano Mangiola. Last updated 5 months ago.

assaydomain infrastructure rnaseq differentialexpression geneexpression normalization clustering qualitycontrol sequencing transcription transcriptomics cytometry genomics tidyverse

64 stars 6.11 score 5 scripts

bioc

peco:A Supervised Approach for Predicting cell Cycle Progression using scRNA-seq data

Our approach provides a way to assign continuous cell cycle phase using scRNA-seq data, and consequently, allows to identify cyclic trend of gene expression levels along the cell cycle. This package provides method and training data, which includes scRNA-seq data collected from 6 individual cell lines of induced pluripotent stem cells (iPSCs), and also continuous cell cycle phase derived from FUCCI fluorescence imaging data.

Maintained by Chiaowen Joyce Hsiao. Last updated 5 months ago.

sequencing rnaseq geneexpression transcriptomics singlecell software statisticalmethod classification visualization cell-cycle single-cell-rna-seq

12 stars 6.09 score 34 scripts

bioc

Dino:Normalization of Single-Cell mRNA Sequencing Data

Dino normalizes single-cell, mRNA sequencing data to correct for technical variation, particularly sequencing depth, prior to downstream analysis. The approach produces a matrix of corrected expression for which the dependency between sequencing depth and the full distribution of normalized expression; many existing methods aim to remove only the dependency between sequencing depth and the mean of the normalized expression. This is particuarly useful in the context of highly sparse datasets such as those produced by 10X genomics and other uninque molecular identifier (UMI) based microfluidics protocols for which the depth-dependent proportion of zeros in the raw expression data can otherwise present a challenge.

Maintained by Jared Brown. Last updated 5 months ago.

software normalization rnaseq singlecell sequencing geneexpression transcriptomics regression cellbasedassays

9 stars 6.02 score 13 scripts

exaexa

EmbedSOM:Fast Embedding Guided by Self-Organizing Map

Provides a smooth mapping of multidimensional points into low-dimensional space defined by a self-organizing map. Designed to work with 'FlowSOM' and flow-cytometry use-cases. See Kratochvil et al. (2019) <doi:10.12688/f1000research.21642.1>.

Maintained by Mirek Kratochvil. Last updated 2 months ago.

cytometry som visualization cpp

26 stars 6.02 score 8 scripts

bioc

dar:Differential Abundance Analysis by Consensus

Differential abundance testing in microbiome data challenges both parametric and non-parametric statistical methods, due to its sparsity, high variability and compositional nature. Microbiome-specific statistical methods often assume classical distribution models or take into account compositional specifics. These produce results that range within the specificity vs sensitivity space in such a way that type I and type II error that are difficult to ascertain in real microbiome data when a single method is used. Recently, a consensus approach based on multiple differential abundance (DA) methods was recently suggested in order to increase robustness. With dar, you can use dplyr-like pipeable sequences of DA methods and then apply different consensus strategies. In this way we can obtain more reliable results in a fast, consistent and reproducible way.

Maintained by Francesc Catala-Moll. Last updated 13 days ago.

software sequencing microbiome metagenomics multiplecomparison normalization bioconductor biomarker-discovery differential-abundance-analysis feature-selection microbiology phyloseq

2 stars 5.98 score 8 scripts

bioc

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

scFeatures constructs multi-view representations of single-cell and spatial data. scFeatures is a tool that generates multi-view representations of single-cell and spatial data through the construction of a total of 17 feature types. These features can then be used for a variety of analyses using other software in Biocondutor.

Maintained by Yue Cao. Last updated 5 months ago.

cellbasedassays singlecell spatial software transcriptomics

10 stars 5.95 score 15 scripts

feiyoung

ProFAST:Probabilistic Factor Analysis for Spatially-Aware Dimension Reduction

Probabilistic factor analysis for spatially-aware dimension reduction across multi-section spatial transcriptomics data with millions of spatial locations. More details can be referred to Wei Liu, et al. (2023) <doi:10.1101/2023.07.11.548486>.

Maintained by Wei Liu. Last updated 2 months ago.

openblas cpp

2 stars 5.86 score 12 scripts 1 dependents

bioc

ChromSCape:Analysis of single-cell epigenomics datasets with a Shiny App

ChromSCape - Chromatin landscape profiling for Single Cells - is a ready-to-launch user-friendly Shiny Application for the analysis of single-cell epigenomics datasets (scChIP-seq, scATAC-seq, scCUT&Tag, ...) from aligned data to differential analysis & gene set enrichment analysis. It is highly interactive, enables users to save their analysis and covers a wide range of analytical steps: QC, preprocessing, filtering, batch correction, dimensionality reduction, vizualisation, clustering, differential analysis and gene set analysis.

Maintained by Pacome Prompsy. Last updated 5 months ago.

shinyapps software singlecell chipseq atacseq methylseq classification clustering epigenetics principalcomponent annotation batcheffect multiplecomparison normalization pathways preprocessing qualitycontrol reportwriting visualization genesetenrichment differentialpeakcalling epigenomics shiny single-cell cpp

14 stars 5.83 score 16 scripts

bioc

scBubbletree:Quantitative visual exploration of scRNA-seq data

scBubbletree is a quantitative method for the visual exploration of scRNA-seq data, preserving key biological properties such as local and global cell distances and cell density distributions across samples. It effectively resolves overplotting and enables the visualization of diverse cell attributes from multiomic single-cell experiments. Additionally, scBubbletree is user-friendly and integrates seamlessly with popular scRNA-seq analysis tools, facilitating comprehensive and intuitive data interpretation.

Maintained by Simo Kitanovski. Last updated 5 months ago.

visualization clustering singlecell transcriptomics rnaseq big-data bigdata scrna-seq scrna-seq-analysis visual visual-exploration

6 stars 5.82 score 8 scripts

bioc

dandelionR:Single-cell Immune Repertoire Trajectory Analysis in R

dandelionR is an R package for performing single-cell immune repertoire trajectory analysis, based on the original python implementation. It provides the necessary functions to interface with scRepertoire and a custom implementation of an absorbing Markov chain for pseudotime inference, inspired by the Palantir Python package.

Maintained by Kelvin Tuong. Last updated 26 days ago.

software immunooncology singlecell

8 stars 5.81 score 7 scripts

bioc

benchdamic:Benchmark of differential abundance methods on microbiome data

Starting from a microbiome dataset (16S or WMS with absolute count values) it is possible to perform several analysis to assess the performances of many differential abundance detection methods. A basic and standardized version of the main differential abundance analysis methods is supplied but the user can also add his method to the benchmark. The analyses focus on 4 main aspects: i) the goodness of fit of each method's distributional assumptions on the observed count data, ii) the ability to control the false discovery rate, iii) the within and between method concordances, iv) the truthfulness of the findings if any apriori knowledge is given. Several graphical functions are available for result visualization.

Maintained by Matteo Calgaro. Last updated 4 months ago.

metagenomics microbiome differentialexpression multiplecomparison normalization preprocessing software benchmark differential-abundance-methods

8 stars 5.78 score 8 scripts

bioc

scRNAseqApp:A single-cell RNAseq Shiny app-package

The scRNAseqApp is a Shiny app package designed for interactive visualization of single-cell data. It is an enhanced version derived from the ShinyCell, repackaged to accommodate multiple datasets. The app enables users to visualize data containing various types of information simultaneously, facilitating comprehensive analysis. Additionally, it includes a user management system to regulate database accessibility for different users.

Maintained by Jianhong Ou. Last updated 15 days ago.

visualization singlecell rnaseq interactive-visualizations multiple-users shiny-apps single-cell-rna-seq

4 stars 5.76 score 3 scripts

core-bioinformatics

ClustAssess:Tools for Assessing Clustering

A set of tools for evaluating clustering robustness using proportion of ambiguously clustered pairs (Senbabaoglu et al. (2014) <doi:10.1038/srep06207>), as well as similarity across methods and method stability using element-centric clustering comparison (Gates et al. (2019) <doi:10.1038/s41598-019-44892-y>). Additionally, this package enables stability-based parameter assessment for graph-based clustering pipelines typical in single-cell data analysis.

Maintained by Andi Munteanu. Last updated 1 months ago.

software singlecell rnaseq atacseq normalization preprocessing dimensionreduction visualization qualitycontrol clustering classification annotation geneexpression differentialexpression bioinformatics genomics machine-learning parameter-optimization robustness single-cell unsupervised-learning cpp

23 stars 5.70 score 18 scripts

xiaozhangryy

CAESAR.Suite:CAESAR: a Cross-Technology and Cross-Resolution Framework for Spatial Omics Annotation

Biotechnology in spatial omics has advanced rapidly over the past few years, enhancing both throughput and resolution. However, existing annotation pipelines in spatial omics predominantly rely on clustering methods, lacking the flexibility to integrate extensive annotated information from single-cell RNA sequencing (scRNA-seq) due to discrepancies in spatial resolutions, species, or modalities. Here we introduce the CAESAR suite, an open-source software package that provides image-based spatial co-embedding of locations and genomic features. It uniquely transfers labels from scRNA-seq reference, enabling the annotation of spatial omics datasets across different technologies, resolutions, species, and modalities, based on the conserved relationship between signature genes and cells/locations at an appropriate level of granularity. Notably, CAESAR enriches location-level pathways, allowing for the detection of gradual biological pathway activation within spatially defined domain types. More details on the methods related to our paper currently under submission. A full reference to the paper will be provided in future versions once the paper is published.

Maintained by Xiao Zhang. Last updated 4 days ago.

openblas cpp

1 stars 5.67 score 2 scripts

kharchenkolab

leidenAlg:Implements the Leiden Algorithm via an R Interface

An R interface to the Leiden algorithm, an iterative community detection algorithm on networks. The algorithm is designed to converge to a partition in which all subsets of all communities are locally optimally assigned, yielding communities guaranteed to be connected. The implementation proves to be fast, scales well, and can be run on graphs of millions of nodes (as long as they can fit in memory). The original implementation was constructed as a python interface "leidenalg" found here: <https://github.com/vtraag/leidenalg>. The algorithm was originally described in Traag, V.A., Waltman, L. & van Eck, N.J. "From Louvain to Leiden: guaranteeing well-connected communities". Sci Rep 9, 5233 (2019) <doi:10.1038/s41598-019-41695-z>.

Maintained by Evan Biederstedt. Last updated 5 months ago.

fortran cpp

9 stars 5.61 score 28 scripts 5 dependents

bioc

scviR:experimental inferface from R to scvi-tools

This package defines interfaces from R to scvi-tools. A vignette works through the totalVI tutorial for analyzing CITE-seq data. Another vignette compares outputs of Chapter 12 of the OSCA book with analogous outputs based on totalVI quantifications. Future work will address other components of scvi-tools, with a focus on building understanding of probabilistic methods based on variational autoencoders.

Maintained by Vincent Carey. Last updated 5 months ago.

infrastructure singlecell dataimport bioconductor cite-seq scverse

6 stars 5.60 score 11 scripts

rezakj

iCellR:Analyzing High-Throughput Single Cell Sequencing Data

A toolkit that allows scientists to work with data from single cell sequencing technologies such as scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST). Single (i) Cell R package ('iCellR') provides unprecedented flexibility at every step of the analysis pipeline, including normalization, clustering, dimensionality reduction, imputation, visualization, and so on. Users can design both unsupervised and supervised models to best suit their research. In addition, the toolkit provides 2D and 3D interactive visualizations, differential expression analysis, filters based on cells, genes and clusters, data merging, normalizing for dropouts, data imputation methods, correcting for batch differences, pathway analysis, tools to find marker genes for clusters and conditions, predict cell types and pseudotime analysis. See Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.05.05.078550> and Khodadadi-Jamayran, et al (2020) <doi:10.1101/2020.03.31.019109> for more details.

Maintained by Alireza Khodadadi-Jamayran. Last updated 9 months ago.

10xgenomics 3d batch-normalization cell-type-classification cite-seq clustering clustering-algorithm diffusion-maps dropout icellr imputation intractive-graph normalization pseudotime scrna-seq scvdj-seq singel-cell-sequencing umap cpp

121 stars 5.56 score 7 scripts 1 dependents

bioc

eiR:Accelerated similarity searching of small molecules

The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach.

Maintained by Thomas Girke. Last updated 2 months ago.

cheminformatics biomedicalinformatics pharmacogenetics pharmacogenomics microtitreplateassay cellbasedassays visualization infrastructure dataimport clustering proteomics metabolomics

3 stars 5.51 score 12 scripts

bioc

scDotPlot:Cluster a Single-cell RNA-seq Dot Plot

Dot plots of single-cell RNA-seq data allow for an examination of the relationships between cell groupings (e.g. clusters) and marker gene expression. The scDotPlot package offers a unified approach to perform a hierarchical clustering analysis and add annotations to the columns and/or rows of a scRNA-seq dot plot. It works with SingleCellExperiment and Seurat objects as well as data frames.

Maintained by Benjamin I Laufer. Last updated 8 days ago.

software visualization differentialexpression geneexpression transcription rnaseq singlecell sequencing clustering

7 stars 5.45 score 2 scripts

bioc

speckle:Statistical methods for analysing single cell RNA-seq data

The speckle package contains functions for the analysis of single cell RNA-seq data. The speckle package currently contains functions to analyse differences in cell type proportions. There are also functions to estimate the parameters of the Beta distribution based on a given counts matrix, and a function to normalise a counts matrix to the median library size. There are plotting functions to visualise cell type proportions and the mean-variance relationship in cell type proportions and counts. As our research into specialised analyses of single cell data continues we anticipate that the package will be updated with new functions.

Maintained by Belinda Phipson. Last updated 5 months ago.

singlecell rnaseq regression geneexpression

5.41 score 258 scripts

bioc

chevreulProcess:Tools for managing SingleCellExperiment objects as projects

Tools analyzing SingleCellExperiment objects as projects. for input into the Chevreul app downstream. Includes functions for analysis of single cell RNA sequencing data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.

Maintained by Kevin Stachelek. Last updated 2 months ago.

coverage rnaseq sequencing visualization geneexpression transcription singlecell transcriptomics normalization preprocessing qualitycontrol dimensionreduction dataimport

5.38 score 2 scripts 2 dependents

bioc

visiumStitched:Enable downstream analysis of Visium capture areas stitched together with Fiji

This package provides helper functions for working with multiple Visium capture areas that overlap each other. This package was developed along with the companion example use case data available from https://github.com/LieberInstitute/visiumStitched_brain. visiumStitched prepares SpaceRanger (10x Genomics) output files so you can stitch the images from groups of capture areas together with Fiji. Then visiumStitched builds a SpatialExperiment object with the stitched data and makes an artificial hexogonal grid enabling the seamless use of spatial clustering methods that rely on such grid to identify neighboring spots, such as PRECAST and BayesSpace. The SpatialExperiment objects created by visiumStitched are compatible with spatialLIBD, which can be used to build interactive websites for stitched SpatialExperiment objects. visiumStitched also enables casting SpatialExperiment objects as Seurat objects.

Maintained by Nicholas J. Eagles. Last updated 4 months ago.

software spatial transcriptomics transcription geneexpression visualization dataimport 10xgenomics bioconductor spatial-transcriptomics spatialexperiment spatiallibd visium

1 stars 5.36 score 4 scripts

zhiyuan-hu-lab

CIDER:Meta-Clustering for scRNA-Seq Integration and Evaluation

A workflow of (a) meta-clustering based on inter-group similarity measures and (b) a ground-truth-free test metric to assess the biological correctness of integration in real datasets. See Hu Z, Ahmed A, Yau C (2021) <doi:10.1101/2021.03.29.437525> for more details.

Maintained by Zhiyuan Hu. Last updated 2 months ago.

5.30 score

bioc

scCB2:CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data

scCB2 is an R package implementing CB2 for distinguishing real cells from empty droplets in droplet-based single cell RNA-seq experiments (especially for 10x Chromium). It is based on clustering similar barcodes and calculating Monte-Carlo p-value for each cluster to test against background distribution. This cluster-level test outperforms single-barcode-level tests in dealing with low count barcodes and homogeneous sequencing library, while keeping FDR well controlled.

Maintained by Zijian Ni. Last updated 5 months ago.

dataimport rnaseq singlecell sequencing geneexpression transcriptomics preprocessing clustering

10 stars 5.30 score 5 scripts

jiang-junyao

CACIMAR:cross-species analysis of cell identities, markers and regulations

A toolkit to perform cross-species analysis based on scRNA-seq data. CACIMAR contains 5 main features. (1) identify Markers in each cluster. (2) Cell type annotaion (3) identify conserved markers. (4) identify conserved cell types. (5) identify conserved modules of regulatory networks.

Maintained by Junyao Jiang. Last updated 4 months ago.

cross-species-analysis scrna-seq

12 stars 5.26 score 6 scripts

bioc

chevreulPlot:Plots used in the chevreulPlot package

Tools for plotting SingleCellExperiment objects in the chevreulPlot package. Includes functions for analysis and visualization of single-cell data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.

Maintained by Kevin Stachelek. Last updated 29 days ago.

coverage rnaseq sequencing visualization geneexpression transcription singlecell transcriptomics normalization preprocessing qualitycontrol dimensionreduction dataimport

5.08 score 2 scripts

bioc

chevreulShiny:Tools for managing SingleCellExperiment objects as projects

Tools for managing SingleCellExperiment objects as projects. Includes functions for analysis and visualization of single-cell data. Also included is a shiny app for visualization of pre-processed scRNA data. Supported by NIH grants R01CA137124 and R01EY026661 to David Cobrinik.

Maintained by Kevin Stachelek. Last updated 25 days ago.

coverage rnaseq sequencing visualization geneexpression transcription singlecell transcriptomics normalization preprocessing qualitycontrol dimensionreduction dataimport

5.08 score

bioc

CDI:Clustering Deviation Index (CDI)

Single-cell RNA-sequencing (scRNA-seq) is widely used to explore cellular variation. The analysis of scRNA-seq data often starts from clustering cells into subpopulations. This initial step has a high impact on downstream analyses, and hence it is important to be accurate. However, there have not been unsupervised metric designed for scRNA-seq to evaluate clustering performance. Hence, we propose clustering deviation index (CDI), an unsupervised metric based on the modeling of scRNA-seq UMI counts to evaluate clustering of cells.

Maintained by Jiyuan Fang. Last updated 5 months ago.

singlecell software clustering visualization sequencing rnaseq cellbasedassays

5 stars 5.00 score 4 scripts

bioc

epiregulon.extra:Companion package to epiregulon with additional plotting, differential and graph functions

Gene regulatory networks model the underlying gene regulation hierarchies that drive gene expression and observed phenotypes. Epiregulon infers TF activity in single cells by constructing a gene regulatory network (regulons). This is achieved through integration of scATAC-seq and scRNA-seq data and incorporation of public bulk TF ChIP-seq data. Links between regulatory elements and their target genes are established by computing correlations between chromatin accessibility and gene expressions.

Maintained by Xiaosai Yao. Last updated 9 days ago.

generegulation network geneexpression transcription chiponchip differentialexpression genetarget normalization graphandnetwork

4.95 score 10 scripts

bioc

decontX:Decontamination of single cell genomics data

This package contains implementation of DecontX (Yang et al. 2020), a decontamination algorithm for single-cell RNA-seq, and DecontPro (Yin et al. 2023), a decontamination algorithm for single cell protein expression data. DecontX is a novel Bayesian method to computationally estimate and remove RNA contamination in individual cells without empty droplet information. DecontPro is a Bayesian method that estimates the level of contamination from ambient and background sources in CITE-seq ADT dataset and decontaminate the dataset.

Maintained by Joshua Campbell. Last updated 1 months ago.

singlecell bayesian cpp

4.94 score 29 scripts

jgasmits

AnanseSeurat:Construct ANANSE GRN-Analysis Seurat

Enables gene regulatory network (GRN) analysis on single cell clusters, using the GRN analysis software 'ANANSE', Xu et al.(2021) <doi:10.1093/nar/gkab598>. Export data from 'Seurat' objects, for GRN analysis by 'ANANSE' implemented in 'snakemake'. Finally, incorporate results for visualization and interpretation.

Maintained by Jos Smits. Last updated 1 years ago.

grn-analysis seurat-objects single-cell single-cell-atac-seq single-cell-rna-seq

8 stars 4.90 score 4 scripts

bioc

CelliD:Unbiased Extraction of Single Cell gene signatures using Multiple Correspondence Analysis

CelliD is a clustering-free multivariate statistical method for the robust extraction of per-cell gene signatures from single-cell RNA-seq. CelliD allows unbiased cell identity recognition across different donors, tissues-of-origin, model organisms and single-cell omics protocols. The package can also be used to explore functional pathways enrichment in single cell data.

Maintained by Akira Cortal. Last updated 5 months ago.

rnaseq singlecell dimensionreduction clustering genesetenrichment geneexpression atacseq openblas cpp openmp

4.85 score 70 scripts

yuelyu21

SCIntRuler:Guiding the Integration of Multiple Single-Cell RNA-Seq Datasets

The accumulation of single-cell RNA-seq (scRNA-seq) studies highlights the potential benefits of integrating multiple datasets. By augmenting sample sizes and enhancing analytical robustness, integration can lead to more insightful biological conclusions. However, challenges arise due to the inherent diversity and batch discrepancies within and across studies. SCIntRuler, a novel R package, addresses these challenges by guiding the integration of multiple scRNA-seq datasets.

Maintained by Yue Lyu. Last updated 5 months ago.

sequencing geneticvariability singlecell cpp

2 stars 4.85 score 3 scripts

papatheodorou-group

scGOclust:Measuring Cell Type Similarity with Gene Ontology in Single-Cell RNA-Seq

Traditional methods for analyzing single cell RNA-seq datasets focus solely on gene expression, but this package introduces a novel approach that goes beyond this limitation. Using Gene Ontology terms as features, the package allows for the functional profile of cell populations, and comparison within and between datasets from the same or different species. Our approach enables the discovery of previously unrecognized functional similarities and differences between cell types and has demonstrated success in identifying cell types' functional correspondence even between evolutionarily distant species.

Maintained by Yuyao Song. Last updated 7 days ago.

9 stars 4.80 score 14 scripts

bioc

airpart:Differential cell-type-specific allelic imbalance

Airpart identifies sets of genes displaying differential cell-type-specific allelic imbalance across cell types or states, utilizing single-cell allelic counts. It makes use of a generalized fused lasso with binomial observations of allelic counts to partition cell types by their allelic imbalance. Alternatively, a nonparametric method for partitioning cell types is offered. The package includes a number of visualizations and quality control functions for examining single cell allelic imbalance datasets.

Maintained by Wancen Mu. Last updated 5 months ago.

singlecell rnaseq atacseq chipseq sequencing generegulation geneexpression transcription transcriptomevariant cellbiology functionalgenomics differentialexpression graphandnetwork regression clustering qualitycontrol

2 stars 4.78 score 2 scripts

bioc

MEB:A normalization-invariant minimum enclosing ball method to detect differentially expressed genes for RNA-seq and scRNA-seq data

This package provides a method to identify differential expression genes in the same or different species. Given that non-DE genes have some similarities in features, a scaling-free minimum enclosing ball (SFMEB) model is built to cover those non-DE genes in feature space, then those DE genes, which are enormously different from non-DE genes, being regarded as outliers and rejected outside the ball. The method on this package is described in the article 'A minimum enclosing ball method to detect differential expression genes for RNA-seq data'. The SFMEB method is extended to the scMEB method that considering two or more potential types of cells or unknown labels scRNA-seq dataset DEGs identification.

Maintained by Jiadi Zhu. Last updated 5 months ago.

differentialexpression geneexpression normalization classification sequencing

4.78 score 1 scripts

bioc

stJoincount:stJoincount - Join count statistic for quantifying spatial correlation between clusters

stJoincount facilitates the application of join count analysis to spatial transcriptomic data generated from the 10x Genomics Visium platform. This tool first converts a labeled spatial tissue map into a raster object, in which each spatial feature is represented by a pixel coded by label assignment. This process includes automatic calculation of optimal raster resolution and extent for the sample. A neighbors list is then created from the rasterized sample, in which adjacent and diagonal neighbors for each pixel are identified. After adding binary spatial weights to the neighbors list, a multi-categorical join count analysis is performed to tabulate "joins" between all possible combinations of label pairs. The function returns the observed join counts, the expected count under conditions of spatial randomness, and the variance calculated under non-free sampling. The z-score is then calculated as the difference between observed and expected counts, divided by the square root of the variance.

Maintained by Jiarong Song. Last updated 5 months ago.

transcriptomics clustering spatial biocviews software

4 stars 4.60 score 3 scripts

colemanrharris

mxnorm:Apply Normalization Methods to Multiplexed Images

Implements methods to normalize multiplexed imaging data, including statistical metrics and visualizations to quantify technical variation in this data type. Reference for methods listed here: Harris, C., Wrobel, J., & Vandekar, S. (2022). mxnorm: An R Package to Normalize Multiplexed Imaging Data. Journal of Open Source Software, 7(71), 4180, <doi:10.21105/joss.04180>.

Maintained by Coleman Harris. Last updated 2 years ago.

7 stars 4.54 score 7 scripts

bioc

MAPFX:MAssively Parallel Flow cytometry Xplorer (MAPFX): A Toolbox for Analysing Data from the Massively-Parallel Cytometry Experiments

MAPFX is an end-to-end toolbox that pre-processes the raw data from MPC experiments (e.g., BioLegend's LEGENDScreen and BD Lyoplates assays), and further imputes the ‘missing’ infinity markers in the wells without those measurements. The pipeline starts by performing background correction on raw intensities to remove the noise from electronic baseline restoration and fluorescence compensation by adapting a normal-exponential convolution model. Unwanted technical variation, from sources such as well effects, is then removed using a log-normal model with plate, column, and row factors, after which infinity markers are imputed using the informative backbone markers as predictors. The completed dataset can then be used for clustering and other statistical analyses. Additionally, MAPFX can be used to normalise data from FFC assays as well.

Maintained by Hsiao-Chi Liao. Last updated 5 months ago.

software flowcytometry cellbasedassays singlecell proteomics clustering

1 stars 4.54 score

bioc

mumosa:Multi-Modal Single-Cell Analysis Methods

Assorted utilities for multi-modal analyses of single-cell datasets. Includes functions to combine multiple modalities for downstream analysis, perform MNN-based batch correction across multiple modalities, and to compute correlations between assay values for different modalities.

Maintained by Aaron Lun. Last updated 5 months ago.

immunooncology singlecell rnaseq

4.51 score 13 scripts

bioc

spillR:Spillover Compensation in Mass Cytometry Data

Channel interference in mass cytometry can cause spillover and may result in miscounting of protein markers. We develop a nonparametric finite mixture model and use the mixture components to estimate the probability of spillover. We implement our method using expectation-maximization to fit the mixture model.

Maintained by Marco Guazzini. Last updated 5 months ago.

flowcytometry immunooncology massspectrometry preprocessing singlecell software statisticalmethod visualization regression

4.48 score 3 scripts

bioc

RCSL:Rank Constrained Similarity Learning for single cell RNA sequencing data

A novel clustering algorithm and toolkit RCSL (Rank Constrained Similarity Learning) to accurately identify various cell types using scRNA-seq data from a complex tissue. RCSL considers both lo-cal similarity and global similarity among the cells to discern the subtle differences among cells of the same type as well as larger differences among cells of different types. RCSL uses Spearman’s rank correlations of a cell’s expression vector with those of other cells to measure its global similar-ity, and adaptively learns neighbour representation of a cell as its local similarity. The overall similar-ity of a cell to other cells is a linear combination of its global similarity and local similarity.

Maintained by Qinglin Mei. Last updated 5 months ago.

singlecell software clustering dimensionreduction rnaseq visualization sequencing

2 stars 4.48 score 10 scripts

bioc

PRONE:The PROteomics Normalization Evaluator

High-throughput omics data are often affected by systematic biases introduced throughout all the steps of a clinical study, from sample collection to quantification. Normalization methods aim to adjust for these biases to make the actual biological signal more prominent. However, selecting an appropriate normalization method is challenging due to the wide range of available approaches. Therefore, a comparative evaluation of unnormalized and normalized data is essential in identifying an appropriate normalization strategy for a specific data set. This R package provides different functions for preprocessing, normalizing, and evaluating different normalization approaches. Furthermore, normalization methods can be evaluated on downstream steps, such as differential expression analysis and statistical enrichment analysis. Spike-in data sets with known ground truth and real-world data sets of biological experiments acquired by either tandem mass tag (TMT) or label-free quantification (LFQ) can be analyzed.

Maintained by Lis Arend. Last updated 7 days ago.

proteomics preprocessing normalization differentialexpression visualization data-analysis evaluation

2 stars 4.41 score 9 scripts

dosorio

rPanglaoDB:Download and Merge Single-Cell RNA-Seq Data from the PanglaoDB Database

Download and merge labeled single-cell RNA-seq data from the PanglaoDB <https://panglaodb.se/> into a Seurat object.

Maintained by Daniel Osorio. Last updated 2 years ago.

data-integration data-mining rna-seq single-cell single-cell-rna-seq

26 stars 4.41 score 20 scripts

niaid

HDStIM:High Dimensional Stimulation Immune Mapping ('HDStIM')

A method for identifying responses to experimental stimulation in mass or flow cytometry that uses high dimensional analysis of measured parameters and can be performed with an end-to-end unsupervised approach. In the context of in vitro stimulation assays where high-parameter cytometry was used to monitor intracellular response markers, using cell populations annotated either through automated clustering or manual gating for a combined set of stimulated and unstimulated samples, 'HDStIM' labels cells as responding or non-responding. The package also provides auxiliary functions to rank intracellular markers based on their contribution to identifying responses and generating diagnostic plots.

Maintained by Rohit Farmer. Last updated 1 years ago.

complexheatmap assay cytof cytometry cytometry-analysis-pipeline flowcytometry stimulation

3 stars 4.41 score 17 scripts

bioc

Spaniel:Spatial Transcriptomics Analysis

Spaniel includes a series of tools to aid the quality control and analysis of Spatial Transcriptomics data. Spaniel can import data from either the original Spatial Transcriptomics system or 10X Visium technology. The package contains functions to create a SingleCellExperiment Seurat object and provides a method of loading a histologial image into R. The spanielPlot function allows visualisation of metrics contained within the S4 object overlaid onto the image of the tissue.

Maintained by Rachel Queen. Last updated 5 months ago.

singlecell rnaseq qualitycontrol preprocessing normalization visualization transcriptomics geneexpression sequencing software dataimport datarepresentation infrastructure coverage clustering

4.34 score 22 scripts

bioc

ClusterFoldSimilarity:Calculate similarity of clusters from different single cell samples using foldchanges

This package calculates a similarity coefficient using the fold changes of shared features (e.g. genes) among clusters of different samples/batches/datasets. The similarity coefficient is calculated using the dot-product (Hadamard product) of every pairwise combination of Fold Changes between a source cluster i of sample/dataset n and all the target clusters j in sample/dataset m

Maintained by Oscar Gonzalez-Velasco. Last updated 5 months ago.

singlecell clustering featureextraction graphandnetwork genetarget rnaseq

4.34 score 11 scripts

bioc

RegionalST:Investigating regions of interest and performing regional cell type-specific analysis with spatial transcriptomics data

This package analyze spatial transcriptomics data through cross-regional cell type-specific analysis. It selects regions of interest (ROIs) and identifys cross-regional cell type-specific differential signals. The ROIs can be selected using automatic algorithm or through manual selection. It facilitates manual selection of ROIs using a shiny application.

Maintained by Ziyi Li. Last updated 4 months ago.

spatial transcriptomics reactome kegg

4.30 score 8 scripts

bioc

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

This package is designed to model gene detection pattern of scRNA-seq through a binary factor analysis model. This model allows user to pass into a cell level covariate matrix X and gene level covariate matrix Q to account for nuisance variance(e.g batch effect), and it will output a low dimensional embedding matrix for downstream analysis.

Maintained by Ruoxin Li. Last updated 5 months ago.

singlecell transcriptomics dimensionreduction geneexpression atacseq batcheffect kegg qualitycontrol

4.30 score 4 scripts

yanpd01

ggsector:Draw Sectors

Some useful functions that can use 'grid' and 'ggplot2' to plot sectors and interact with 'Seurat' to plot gene expression percentages. Also, there are some examples of how to draw sectors in 'ComplexHeatmap'.

Maintained by Pengdong Yan. Last updated 5 months ago.

4 stars 4.30 score 5 scripts

bioc

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

cytofQC is a package for initial cleaning of CyTOF data. It uses a semi-supervised approach for labeling cells with their most likely data type (bead, doublet, debris, dead) and the probability that they belong to each label type. This package does not remove data from the dataset, but provides labels and information to aid the data user in cleaning their data. Our algorithm is able to distinguish between doublets and large cells.

Maintained by Jill Lundell. Last updated 5 months ago.

software singlecell annotation

2 stars 4.30 score 3 scripts

cyrillagger

scDiffCom:Differential Analysis of Intercellular Communication from scRNA-Seq Data

Analysis tools to investigate changes in intercellular communication from scRNA-seq data. Using a Seurat object as input, the package infers which cell-cell interactions are present in the dataset and how these interactions change between two conditions of interest (e.g. young vs old). It relies on an internal database of ligand-receptor interactions (available for human, mouse and rat) that have been gathered from several published studies. Detection and differential analyses rely on permutation tests. The package also contains several tools to perform over-representation analysis and visualize the results. See Lagger, C. et al. (2023) <doi:10.1038/s43587-023-00514-x> for a full description of the methodology.

Maintained by Cyril Lagger. Last updated 1 years ago.

21 stars 4.25 score 17 scripts

ruzhangzhao

mixhvg:Mixture of Multiple Highly Variable Feature Selection Methods

Highly variable gene selection methods, including popular public available methods, and also the mixture of multiple highly variable gene selection methods, <https://github.com/RuzhangZhao/mixhvg>. Reference: <doi:10.1101/2024.08.25.608519>.

Maintained by Ruzhang Zhao. Last updated 26 days ago.

rna-seq-analysis rna-seq-pipeline single-cell single-cell-rna-seq variable-selection

5 stars 4.18 score 6 scripts

khodosevichlab

CRMetrics:Cell Ranger Output Filtering and Metrics Visualization

Sample and cell filtering as well as visualisation of output metrics from 'Cell Ranger' by Grace X.Y. Zheng et al. (2017) <doi:10.1038/ncomms14049>. 'CRMetrics' allows for easy plotting of output metrics across multiple samples as well as comparative plots including statistical assessments of these. 'CRMetrics' allows for easy removal of ambient RNA using 'SoupX' by Matthew D Young and Sam Behjati (2020) <doi:10.1093/gigascience/giaa151> or 'CellBender' by Stephen J Fleming et al. (2022) <doi:10.1101/791699>. Furthermore, it is possible to preprocess data using 'Pagoda2' by Nikolas Barkas et al. (2021) <https://github.com/kharchenkolab/pagoda2> or 'Seurat' by Yuhan Hao et al. (2021) <doi:10.1016/j.cell.2021.04.048> followed by embedding of cells using 'Conos' by Nikolas Barkas et al. (2019) <doi:10.1038/s41592-019-0466-z>. Finally, doublets can be detected using 'scrublet' by Samuel L. Wolock et al. (2019) <doi:10.1016/j.cels.2018.11.005> or 'DoubletDetection' by Gayoso et al. (2020) <doi:10.5281/zenodo.2678041>. In the end, cells are filtered based on user input for use in downstream applications.

Maintained by Rasmus Rydbirk. Last updated 5 months ago.

5 stars 4.18 score 8 scripts

bioc

partCNV:Infer locally aneuploid cells using single cell RNA-seq data

This package uses a statistical framework for rapid and accurate detection of aneuploid cells with local copy number deletion or amplification. Our method uses an EM algorithm with mixtures of Poisson distributions while incorporating cytogenetics information (e.g., regional deletion or amplification) to guide the classification (partCNV). When applicable, we further improve the accuracy by integrating a Hidden Markov Model for feature selection (partCNVH).

Maintained by Ziyi Li. Last updated 5 months ago.

software copynumbervariation hiddenmarkovmodel singlecell classification

4.18 score 4 scripts

rikenbit

WormTensor:A Clustering Method for Time-Series Whole-Brain Activity Data of 'C. elegans'

A toolkit to detect clusters from distance matrices. The distance matrices are assumed to be calculated between the cells of multiple animals ('Caenorhabditis elegans') from input time-series matrices. Some functions for generating distance matrices, performing clustering, evaluating the clustering, and visualizing the results of clustering and evaluation are available. We're also providing the download function to retrieve the calculated distance matrices from 'figshare' <https://figshare.com>.

Maintained by Kentaro Yamamoto. Last updated 8 months ago.

1 stars 4.18 score 3 scripts

kzst

nda:Generalized Network-Based Dimensionality Reduction and Analysis

Non-parametric dimensionality reduction function. Reduction with and without feature selection. Plot functions. Automated feature selections. Kosztyan et. al. (2024) <doi:10.1016/j.eswa.2023.121779>.

Maintained by Zsolt T. Kosztyan. Last updated 1 months ago.

2 stars 4.08 score 1 scripts

bioc

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

scTreeViz provides classes to support interactive data aggregation and visualization of single cell RNA-seq datasets with hierarchies for e.g. cell clusters at different resolutions. The `TreeIndex` class provides methods to manage hierarchy and split the tree at a given resolution or across resolutions. The `TreeViz` class extends `SummarizedExperiment` and can performs quick aggregations on the count matrix defined by clusters.

Maintained by Jayaram Kancherla. Last updated 5 months ago.

visualization infrastructure gui singlecell

4.00 score 3 scripts

bioc

VAExprs:Generating Samples of Gene Expression Data with Variational Autoencoders

A fundamental problem in biomedical research is the low number of observations, mostly due to a lack of available biosamples, prohibitive costs, or ethical reasons. By augmenting a few real observations with artificially generated samples, their analysis could lead to more robust and higher reproducible. One possible solution to the problem is the use of generative models, which are statistical models of data that attempt to capture the entire probability distribution from the observations. Using the variational autoencoder (VAE), a well-known deep generative model, this package is aimed to generate samples with gene expression data, especially for single-cell RNA-seq data. Furthermore, the VAE can use conditioning to produce specific cell types or subpopulations. The conditional VAE (CVAE) allows us to create targeted samples rather than completely random ones.

Maintained by Dongmin Jung. Last updated 5 months ago.

software geneexpression singlecell openjdk

4.00 score 4 scripts

fentouxungui

SeuratExplorer:An 'Shiny' App for Exploring scRNA-seq Data Processed in 'Seurat'

A simple, one-command package which runs an interactive dashboard capable of common visualizations for single cell RNA-seq. 'SeuratExplorer' requires a processed 'Seurat' object, which is saved as 'rds' or 'qs2' file.

Maintained by Yongchao Zhang. Last updated 10 hours ago.

3.95 score

joycekang

symphony:Efficient and Precise Single-Cell Reference Atlas Mapping

Implements the Symphony single-cell reference building and query mapping algorithms and additional functions described in Kang et al <https://www.nature.com/articles/s41467-021-25957-x>.

Maintained by Joyce Kang. Last updated 2 years ago.

openblas cpp

3.83 score 134 scripts

bioc

DESpace:DESpace: a framework to discover spatially variable genes and differential spatial patterns across conditions

Intuitive framework for identifying spatially variable genes (SVGs) and differential spatial variable pattern (DSP) between conditions via edgeR, a popular method for performing differential expression analyses. Based on pre-annotated spatial clusters as summarized spatial information, DESpace models gene expression using a negative binomial (NB), via edgeR, with spatial clusters as covariates. SVGs are then identified by testing the significance of spatial clusters. For multi-sample, multi-condition datasets, we again fit a NB model via edgeR, incorporating spatial clusters, conditions and their interactions as covariates. DSP genes-representing differences in spatial gene expression patterns across experimental conditions-are identified by testing the interaction between spatial clusters and conditions.

Maintained by Peiying Cai. Last updated 9 days ago.

spatial singlecell rnaseq transcriptomics geneexpression sequencing differentialexpression statisticalmethod visualization

4 stars 3.72 score 13 scripts

cran

Platypus:Single-Cell Immune Repertoire and Gene Expression Analysis

We present 'Platypus', an open-source software platform providing a user-friendly interface to investigate B-cell receptor and T-cell receptor repertoires from scSeq experiments. 'Platypus' provides a framework to automate and ease the analysis of single-cell immune repertoires while also incorporating transcriptional information involving unsupervised clustering, gene expression and gene ontology. This R version of 'Platypus' is part of the 'ePlatypus' ecosystem for computational analysis of immunogenomics data: Yermanos et al. (2021) <doi:10.1093/nargab/lqab023>, Cotet et al. (2023) <doi:10.1093/bioinformatics/btad553>.

Maintained by Alexander Yermanos. Last updated 5 months ago.

3.70 score

sistia01

DWLS:Gene Expression Deconvolution Using Dampened Weighted Least Squares

The rapid development of single-cell transcriptomic technologies has helped uncover the cellular heterogeneity within cell populations. However, bulk RNA-seq continues to be the main workhorse for quantifying gene expression levels due to technical simplicity and low cost. To most effectively extract information from bulk data given the new knowledge gained from single-cell methods, we have developed a novel algorithm to estimate the cell-type composition of bulk data from a single-cell RNA-seq-derived cell-type signature. Comparison with existing methods using various real RNA-seq data sets indicates that our new approach is more accurate and comprehensive than previous methods, especially for the estimation of rare cell types. More importantly,our method can detect cell-type composition changes in response to external perturbations, thereby providing a valuable, cost-effective method for dissecting the cell-type-specific effects of drug treatments or condition changes. As such, our method is applicable to a wide range of biological and clinical investigations. Dampened weighted least squares ('DWLS') is an estimation method for gene expression deconvolution, in which the cell-type composition of a bulk RNA-seq data set is computationally inferred. This method corrects common biases towards cell types that are characterized by highly expressed genes and/or are highly prevalent, to provide accurate detection across diverse cell types. See: <https://www.nature.com/articles/s41467-019-10802-z.pdf> for more information about the development of 'DWLS' and the methods behind our functions.

Maintained by Adriana Sistig. Last updated 3 years ago.

2 stars 3.62 score 42 scripts

bioc

infinityFlow:Augmenting Massively Parallel Cytometry Experiments Using Multivariate Non-Linear Regressions

Pipeline to analyze and merge data files produced by BioLegend's LEGENDScreen or BD Human Cell Surface Marker Screening Panel (BD Lyoplates).

Maintained by Etienne Becht. Last updated 5 months ago.

software flowcytometry cellbasedassays singlecell proteomics

3.60 score 4 scripts

liuy12

SCdeconR:Deconvolution of Bulk RNA-Seq Data using Single-Cell RNA-Seq Data as Reference

Streamlined workflow from deconvolution of bulk RNA-seq data to downstream differential expression and gene-set enrichment analysis. Provide various visualization functions.

Maintained by Yuanhang Liu. Last updated 10 months ago.

bulk-rna-seq-deconvolution deconvolution differential-expression ffpe geneset-enrichment-analysis scdeconr single-cell

4 stars 3.60 score 4 scripts

erhard-lab

HetSeq:Identifying Modulators of Cellular Responses Leveraging Intercellular Heterogeneity

Cellular responses to perturbations are highly heterogeneous and depend largely on the initial state of cells. Connecting post-perturbation cells via cellular trajectories to untreated cells (e.g. by leveraging metabolic labeling information) enables exploitation of intercellular heterogeneity as a combined knock-down and overexpression screen to identify pathway modulators, termed Heterogeneity-seq (see 'Berg et al' <doi:10.1101/2024.10.28.620481>). This package contains functions to generate cellular trajectories based on scSLAM-seq (single-cell, thiol-(SH)-linked alkylation of RNA for metabolic labelling sequencing) time courses, functions to identify pathway modulators and to visualize the results.

Maintained by Kevin Berg. Last updated 2 months ago.

3.54 score

bioc

SCArray.sat:Large-scale single-cell RNA-seq data analysis using GDS files and Seurat

Extends the Seurat classes and functions to support Genomic Data Structure (GDS) files as a DelayedArray backend for data representation. It relies on the implementation of GDS-based DelayedMatrix in the SCArray package to represent single cell RNA-seq data. The common optimized algorithms leveraging GDS-based and single cell-specific DelayedMatrix (SC_GDSMatrix) are implemented in the SCArray package. SCArray.sat introduces a new SCArrayAssay class (derived from the Seurat Assay), which wraps raw counts, normalized expressions and scaled data matrix based on GDS-specific DelayedMatrix. It is designed to integrate seamlessly with the Seurat package to provide common data analysis in the SeuratObject-based workflow. Compared with Seurat, SCArray.sat significantly reduces the memory usage without downsampling and can be applied to very large datasets.

Maintained by Xiuwen Zheng. Last updated 4 days ago.

datarepresentation dataimport singlecell rnaseq

1 stars 3.48 score 3 scripts

thecailab

SCRIP:An Accurate Simulator for Single-Cell RNA Sequencing Data

We provide a comprehensive scheme that is capable of simulating Single Cell RNA Sequencing data for various parameters of Biological Coefficient of Variation, busting kinetics, differential expression (DE), cell or sample groups, cell trajectory, batch effect and other experimental designs. 'SCRIP' proposed and compared two frameworks with Gamma-Poisson and Beta-Gamma-Poisson models for simulating Single Cell RNA Sequencing data. Other reference is available in Zappia et al. (2017) <https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1305-0>.

Maintained by Fei Qin. Last updated 2 years ago.

2 stars 3.41 score 13 scripts

dsokolo

scMappR:Single Cell Mapper

The single cell mapper (scMappR) R package contains a suite of bioinformatic tools that provide experimentally relevant cell-type specific information to a list of differentially expressed genes (DEG). The function "scMappR_and_pathway_analysis" reranks DEGs to generate cell-type specificity scores called cell-weighted fold-changes. Users input a list of DEGs, normalized counts, and a signature matrix into this function. scMappR then re-weights bulk DEGs by cell-type specific expression from the signature matrix, cell-type proportions from RNA-seq deconvolution and the ratio of cell-type proportions between the two conditions to account for changes in cell-type proportion. With cwFold-changes calculated, scMappR uses two approaches to utilize cwFold-changes to complete cell-type specific pathway analysis. The "process_dgTMatrix_lists" function in the scMappR package contains an automated scRNA-seq processing pipeline where users input scRNA-seq count data, which is made compatible for scMappR and other R packages that analyze scRNA-seq data. We further used this to store hundreds up regularly updating signature matrices. The functions "tissue_by_celltype_enrichment", "tissue_scMappR_internal", and "tissue_scMappR_custom" combine these consistently processed scRNAseq count data with gene-set enrichment tools to allow for cell-type marker enrichment of a generic gene list (e.g. GWAS hits). Reference: Sokolowski,D.J., Faykoo-Martinez,M., Erdman,L., Hou,H., Chan,C., Zhu,H., Holmes,M.M., Goldenberg,A. and Wilson,M.D. (2021) Single-cell mapper (scMappR): using scRNA-seq to infer cell-type specificities of differentially expressed genes. NAR Genomics and Bioinformatics. 3(1). Iqab011. <doi:10.1093/nargab/lqab011>.

Maintained by Dustin Sokolowski. Last updated 2 years ago.

4 stars 3.30 score 9 scripts

shufeyangyi2015310117

SC.MEB:Spatial Clustering with Hidden Markov Random Field using Empirical Bayes

Spatial clustering with hidden markov random field fitted via EM algorithm, details of which can be found in Yi Yang (2021) <doi:10.1101/2021.06.05.447181>. It is not only computationally efficient and scalable to the sample size increment, but also is capable of choosing the smoothness parameter and the number of clusters as well.

Maintained by Yi Yang. Last updated 3 years ago.

openblas cpp

3.04 score 11 scripts

obenno

scSpotlight:A Single Cell Analysis Shiny App

A single cell analysis (viewer) app based on Seurat.

Maintained by Zhixia Xiao. Last updated 7 months ago.

seurat shiny-apps single-cell

2 stars 2.78 score

mohmedsoudy

ScRNAIMM:Performing Single-Cell RNA-Seq Imputation by Using Mean/Median Imputation

Performing single-cell imputation in a way that preserves the biological variations in the data. The package clusters the input data to do imputation for each cluster, and do a distribution check using the Anderson-Darling normality test to impute dropouts using mean or median (Yazici, B., & Yolacan, S. (2007) <DOI:10.1080/10629360600678310>).

Maintained by Mohamed Soudy. Last updated 1 years ago.

2.70 score

sridhara-omics

scPipeline:A Wrapper for 'Seurat' and Related R Packages for End-to-End Single Cell Analysis

Reports markers list, differentially expressed genes, associated pathways, cell-type annotations, does batch correction and other related single cell analyses all wrapped within 'Seurat'.

Maintained by Viswanadham Sridhara. Last updated 21 days ago.

2.70 score

strancsus

scCAN:Single-Cell Clustering using Autoencoder and Network Fusion

A single-cell Clustering method using 'Autoencoder' and Network fusion ('scCAN') Bang Tran (2022) <doi:10.1038/s41598-022-14218-6> for segregating the cells from the high-dimensional 'scRNA-Seq' data. The software automatically determines the optimal number of clusters and then partitions the cells in a way such that the results are robust to noise and dropouts. 'scCAN' is fast and it supports Windows, Linux, and Mac OS.

Maintained by Bang Tran. Last updated 10 months ago.

2.70 score

yuepan027

scpoisson:Single Cell Poisson Probability Paradigm

Useful to visualize the Poissoneity (an independent Poisson statistical framework, where each RNA measurement for each cell comes from its own independent Poisson distribution) of Unique Molecular Identifier (UMI) based single cell RNA sequencing (scRNA-seq) data, and explore cell clustering based on model departure as a novel data representation.

Maintained by Yue Pan. Last updated 3 years ago.

2.70 score 4 scripts

schiebout

CAMML:Cell-Typing using Variance Adjusted Mahalanobis Distances with Multi-Labeling

Creates multi-label cell-types for single-cell RNA-sequencing data based on weighted VAM scoring of cell-type specific gene sets. Schiebout, Frost (2022) <https://psb.stanford.edu/psb-online/proceedings/psb22/schiebout.pdf>.

Maintained by Courtney Schiebout. Last updated 1 years ago.

2.60 score

cran

BioM2:Biologically Explainable Machine Learning Framework

Biologically Explainable Machine Learning Framework for Phenotype Prediction using omics data described in Chen and Schwarz (2017) <doi:10.48550/arXiv.1712.00336>.Identifying reproducible and interpretable biological patterns from high-dimensional omics data is a critical factor in understanding the risk mechanism of complex disease. As such, explainable machine learning can offer biological insight in addition to personalized risk scoring.In this process, a feature space of biological pathways will be generated, and the feature space can also be subsequently analyzed using WGCNA (Described in Horvath and Zhang (2005) <doi:10.2202/1544-6115.1128> and Langfelder and Horvath (2008) <doi:10.1186/1471-2105-9-559> ) methods.

Maintained by Shunjie Zhang. Last updated 1 months ago.

2.54 score

igordot

scooter:Streamlined scRNA-Seq Analysis Pipeline

Streamlined scRNA-Seq analysis pipeline.

Maintained by Igor Dolgalev. Last updated 1 years ago.

4 stars 2.51 score 16 scripts

cran

SPECK:Receptor Abundance Estimation using Reduced Rank Reconstruction and Clustered Thresholding

Surface Protein abundance Estimation using CKmeans-based clustered thresholding ('SPECK') is an unsupervised learning-based method that performs receptor abundance estimation for single cell RNA-sequencing data based on reduced rank reconstruction (RRR) and a clustered thresholding mechanism. Seurat's normalization method is described in: Hao et al., (2021) <doi:10.1016/j.cell.2021.04.048>, Stuart et al., (2019) <doi:10.1016/j.cell.2019.05.031>, Butler et al., (2018) <doi:10.1038/nbt.4096> and Satija et al., (2015) <doi:10.1038/nbt.3192>. Method for the RRR is further detailed in: Erichson et al., (2019) <doi:10.18637/jss.v089.i11> and Halko et al., (2009) <arXiv:0909.4061>. Clustering method is outlined in: Song et al., (2020) <doi:10.1093/bioinformatics/btaa613> and Wang et al., (2011) <doi:10.32614/RJ-2011-015>.

Maintained by Azka Javaid. Last updated 1 years ago.

2.48 score 1 dependents

cran

scaper:Single Cell Transcriptomics-Level Cytokine Activity Prediction and Estimation

Generates cell-level cytokine activity estimates using relevant information from gene sets constructed with the 'CytoSig' and the 'Reactome' databases and scored using the modified 'Variance-adjusted Mahalanobis (VAM)' framework for single-cell RNA-sequencing (scRNA-seq) data. 'CytoSig' database is described in: Jiang at al., (2021) <doi:10.1038/s41592-021-01274-5>. 'Reactome' database is described in: Gillespie et al., (2021) <doi:10.1093/nar/gkab1028>. The 'VAM' method is outlined in: Frost (2020) <doi:10.1093/nar/gkaa582>.

Maintained by Azka Javaid. Last updated 1 years ago.

2.30 score

igordot

phenomenalist:Analysis Toolkit for PhenoCycler (CODEX) Data in R

A collection of tools for cleaning, clustering, and plotting PhenoCycler (CODEX) data.

Maintained by Igor Dolgalev. Last updated 1 years ago.

codex phenocycler

3 stars 2.18 score 1 scripts

cran

PoweREST:A Bootstrap-Based Power Estimation Tool for Spatial Transcriptomics

Power estimation and sample size calculation for 10X Visium Spatial Transcriptomics data to detect differential expressed genes between two conditions based on bootstrap resampling. See Shui et al. (2024) <doi:10.1101/2024.08.30.610564> for method details.

Maintained by Lan Shui. Last updated 7 months ago.

2.00 score

ubcxzhang

scAnnotate:An Automated Cell Type Annotation Tool for Single-Cell RNA-Sequencing Data

An entirely data-driven cell type annotation tools, which requires training data to learn the classifier, but not biological knowledge to make subjective decisions. It consists of three steps: preprocessing training and test data, model fitting on training data, and cell classification on test data. See Xiangling Ji,Danielle Tsao, Kailun Bai, Min Tsao, Li Xing, Xuekui Zhang.(2022)<doi:10.1101/2022.02.19.481159> for more details.

Maintained by Xuekui Zhang. Last updated 1 years ago.

2.00 score 4 scripts

cran

STREAK:Receptor Abundance Estimation using Feature Selection and Gene Set Scoring

Performs receptor abundance estimation for single cell RNA-sequencing data using a supervised feature selection mechanism and a thresholded gene set scoring procedure. Seurat's normalization method is described in: Hao et al., (2021) <doi:10.1016/j.cell.2021.04.048>, Stuart et al., (2019) <doi:10.1016/j.cell.2019.05.031>, Butler et al., (2018) <doi:10.1038/nbt.4096> and Satija et al., (2015) <doi:10.1038/nbt.3192>. Method for reduced rank reconstruction and rank-k selection is detailed in: Javaid et al., (2022) <doi:10.1101/2022.10.08.511197>. Gene set scoring procedure is described in: Frost et al., (2020) <doi:10.1093/nar/gkaa582>. Clustering method is outlined in: Song et al., (2020) <doi:10.1093/bioinformatics/btaa613> and Wang et al., (2011) <doi:10.32614/RJ-2011-015>.

Maintained by Azka Javaid. Last updated 1 years ago.

2.00 score 2 scripts

welch-lab

SiNMFiD:Supervised iNMF informed Deconvolution

A package for completing cell type deconvolution on bulk spatial transcriptomic data utilizing multiple reference scRNA-seq datasets.

Maintained by Joshua Sodicoff. Last updated 1 years ago.

2.00 score 1 scripts

j-mitchel

scITD:Single-Cell Interpretable Tensor Decomposition

Single-cell Interpretable Tensor Decomposition (scITD) employs the Tucker tensor decomposition to extract multicell-type gene expression patterns that vary across donors/individuals. This tool is geared for use with single-cell RNA-sequencing datasets consisting of many source donors. The method has a wide range of potential applications, including the study of inter-individual variation at the population-level, patient sub-grouping/stratification, and the analysis of sample-level batch effects. Each "multicellular process" that is extracted consists of (A) a multi cell type gene loadings matrix and (B) a corresponding donor scores vector indicating the level at which the corresponding loadings matrix is expressed in each donor. Additional methods are implemented to aid in selecting an appropriate number of factors and to evaluate stability of the decomposition. Additional tools are provided for downstream analysis, including integration of gene set enrichment analysis and ligand-receptor analysis. Tucker, L.R. (1966) <doi:10.1007/BF02289464>. Unkel, S., Hannachi, A., Trendafilov, N. T., & Jolliffe, I. T. (2011) <doi:10.1007/s13253-011-0055-9>. Zhou, G., & Cichocki, A. (2012) <doi:10.2478/v10175-012-0051-4>.

Maintained by Jonathan Mitchel. Last updated 2 years ago.

cpp

1.98 score 19 scripts

dzhang777

SlideCNA:Calls Copy Number Alterations from Slide-Seq Data

This takes spatial single-cell-type RNA-seq data (specifically designed for Slide-seq v2) that calls copy number alterations (CNAs) using pseudo-spatial binning, clusters cellular units (e.g. beads) based on CNA profile, and visualizes spatial CNA patterns. Documentation about 'SlideCNA' is included in the the pre-print by Zhang et al. (2022, <doi:10.1101/2022.11.25.517982>). The package 'enrichR' (>= 3.0), conditionally used to annotate SlideCNA-determined clusters with gene ontology terms, can be installed at <https://github.com/wjawaid/enrichR> or with install_github("wjawaid/enrichR").

Maintained by Diane Zhang. Last updated 2 months ago.

1.70 score 3 scripts

blaserlab

blaseRdata:Supporting Data for the blaseRtools Package

What the package does (one paragraph).

Maintained by Brad Blaser. Last updated 1 years ago.

1.70 score 6 scripts

lbosshard

scROSHI:Robust Supervised Hierarchical Identification of Single Cells

Identifying cell types based on expression profiles is a pillar of single cell analysis. 'scROSHI' identifies cell types based on expression profiles of single cell analysis by utilizing previously obtained cell type specific gene sets. It takes into account the hierarchical nature of cell type relationship and does not require training or annotated data. A detailed description of the method can be found at: Prummer, Bertolini, Bosshard, Barkmann, Yates, Boeva, The Tumor Profiler Consortium, Stekhoven, and Singer (2022) <doi:10.1101/2022.04.05.487176>.

Maintained by Lars Bosshard. Last updated 2 years ago.

1.70 score 9 scripts

cran

SpaCCI:Spatially Aware Cell-Cell Interaction Analysis

Provides tools for analyzing spatial cell-cell interactions based on ligand-receptor pairs, including functions for local, regional, and global analysis using spatial transcriptomics data. Integrates with databases like 'CellChat' <http://www.cellchat.org/>, 'CellPhoneDB' <https://www.cellphonedb.org/>, 'Cellinker' <https://www.rna-society.org/cellinker/>, 'ICELLNET' <https://github.com/soumelis-lab/ICELLNET>, and 'ConnectomeDB' <https://humanconnectome.org/software/connectomedb/> to identify ligand-receptor pairs, visualize interactions through heatmaps, chord diagrams, and infer interactions on different spatial scales.

Maintained by Li-Ting Ku. Last updated 2 months ago.

openblas cpp

1.48 score

mohmedsoudy

sccca:Single-Cell Correlation Based Cell Type Annotation

Performing cell type annotation based on cell markers from a unified database. The approach utilizes correlation-based approach combined with association analysis using Fisher-exact and phyper statistical tests (Upton, Graham JG. (1992) <DOI:10.2307/2982890>).

Maintained by Mohamed Soudy. Last updated 1 years ago.

1.00 score

stefanpeidli

scperturbR:E-Statistics for Seurat Objects

R version of 'scperturb' tool for single-cell perturbation analysis. Contains wrappers for performing E-statistics for Seurat objects. More details on the method can be found in Peidli et al. (2023) <doi:10.1101/2022.08.20.504663> and in Székely and Rizzo (2004).

Maintained by Stefan Peidli. Last updated 2 years ago.

1.00 score 7 scripts

xiayh17

scRNAstat:A Pipeline to Process Single Cell RNAseq Data

A pipeline that can process single or multiple Single Cell RNAseq samples primarily specializes in Clustering and Dimensionality Reduction. Meanwhile we use common cell type marker genes for T cells, B cells, Myeloid cells, Epithelial cells, and stromal cells (Fiboblast, Endothelial cells, Pericyte, Smooth muscle cells) to visualize the Seurat clusters, to facilitate labeling them by biological names. Once users named each cluster, they can evaluate the quality of them again and find the de novo marker genes also.

Maintained by Yonghe Xia. Last updated 20 days ago.

1.00 score 2 scripts

Seurat:Tools for Single Cell Genomics

uwot:The Uniform Manifold Approximation and Projection (UMAP) Method for Dimensionality Reduction

scDblFinder:scDblFinder

mia:Microbiome analysis

scater:Single-Cell Analysis Toolkit for Gene Expression Data in R

CATALYST:Cytometry dATa anALYSis Tools

infercnv:Infer Copy Number Variation from Single-Cell RNA-Seq Data

rliger:Linked Inference of Genomic Experimental Relationships

celda:CEllular Latent Dirichlet Allocation

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

singleCellTK:Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

SoupX:Single Cell mRNA Soup eXterminator

MOFA2:Multi-Omics Factor Analysis v2

scMerge:scMerge: Merging multiple batches of scRNA-seq data

tidyseurat:Brings Seurat to the Tidyverse

embed:Extra Recipes for Encoding Predictors

Banksy:Spatial transcriptomic clustering

BayesSpace:Clustering and Resolution Enhancement of Spatial Transcriptomes

miaViz:Microbiome Analysis Plotting and Visualization

M3Drop:Michaelis-Menten Modelling of Dropouts in single-cell RNASeq

SIMLR:Single-cell Interpretation via Multi-kernel LeaRning (SIMLR)

scCustomize:Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

lefser:R implementation of the LEfSE method for microbiome biomarker discovery

scGate:Marker-Based Cell Type Purification for Single-Cell Sequencing Data

fastTopics:Fast Algorithms for Fitting Topic Models and Non-Negative Matrix Factorizations to Count Data

flashier:Empirical Bayes Matrix Factorization

POMA:Tools for Omics Data Analysis

pagoda2:Single Cell Analysis and Differential Expression

FLAMES:FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data

COTAN:COexpression Tables ANalysis

MGnifyR:R interface to EBI MGnify metagenomics resource

ggsc:Visualizing Single Cell and Spatial Transcriptomics

MOSim:Multi-Omics Simulation (MOSim)

netSmooth:Network smoothing for scRNAseq

conos:Clustering on Network of Samples

CuratedAtlasQueryR:Queries the Human Cell Atlas

pipeComp:pipeComp pipeline benchmarking framework

musicatk:Mutational Signature Comprehensive Analysis Toolkit

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

CiteFuse:CiteFuse: multi-modal analysis of CITE-seq data

GeneNMF:Non-Negative Matrix Factorization for Single-Cell Omics

tricycle:tricycle: Transferable Representation and Inference of cell cycle

SpotClean:SpotClean adjusts for spot swapping in spatial transcriptomics data

condiments:Differential Topology, Progression and Differentiation

CatsCradle:This package provides methods for analysing spatial transcriptomics data and for discovering gene clusters

sccore:Core Utilities for Single-Cell RNA-Seq

SignacX:Cell Type Identification and Discovery from Single Cell Gene Expression Data

APackOfTheClones:Visualization of Clonal Expansion for Single Cell Immune Profiles

nebula:Negative Binomial Mixed Models Using Large-Sample Approximation for Differential Expression Analysis of ScRNA-Seq Data

scDHA:Single-Cell Decomposition using Hierarchical Autoencoder

distinct:distinct: a method for differential analyses via hierarchical permutation tests

CellMixS:Evaluate Cellspecific Mixing

scDataviz:scDataviz: single cell dataviz and downstream analyses

iSEEtree:Interactive visualisation for microbiome data

DR.SC:Joint Dimension Reduction and Spatial Clustering

tidyomics:Easily install and load the tidyomics ecosystem

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

Dino:Normalization of Single-Cell mRNA Sequencing Data

EmbedSOM:Fast Embedding Guided by Self-Organizing Map

dar:Differential Abundance Analysis by Consensus

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

ProFAST:Probabilistic Factor Analysis for Spatially-Aware Dimension Reduction

ChromSCape:Analysis of single-cell epigenomics datasets with a Shiny App

scBubbletree:Quantitative visual exploration of scRNA-seq data

dandelionR:Single-cell Immune Repertoire Trajectory Analysis in R

benchdamic:Benchmark of differential abundance methods on microbiome data

scRNAseqApp:A single-cell RNAseq Shiny app-package

ClustAssess:Tools for Assessing Clustering

CAESAR.Suite:CAESAR: a Cross-Technology and Cross-Resolution Framework for Spatial Omics Annotation

leidenAlg:Implements the Leiden Algorithm via an R Interface

scviR:experimental inferface from R to scvi-tools

iCellR:Analyzing High-Throughput Single Cell Sequencing Data

eiR:Accelerated similarity searching of small molecules

scDotPlot:Cluster a Single-cell RNA-seq Dot Plot

speckle:Statistical methods for analysing single cell RNA-seq data

chevreulProcess:Tools for managing SingleCellExperiment objects as projects

visiumStitched:Enable downstream analysis of Visium capture areas stitched together with Fiji

CIDER:Meta-Clustering for scRNA-Seq Integration and Evaluation

scCB2:CB2 improves power of cell detection in droplet-based single-cell RNA sequencing data

CACIMAR:cross-species analysis of cell identities, markers and regulations

peco:A Supervised Approach for Predicting cell Cycle Progression using scRNA-seq data