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single-cell-rna-seq x

65 search results found

Seurat ⭐ 2,025

R toolkit for single cell genomics

Nichenetr ⭐ 416

NicheNet: predict active ligand-target links between interacting cells

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

Multi-subject Single Cell Deconvolution

Dittoseq ⭐ 153

Color blindness friendly visualization of single-cell and bulk RNA-sequencing data

Sccustomize ⭐ 142

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

Tidyseurat ⭐ 131

Seurat meets tidyverse. The best of both worlds.

Haplotype-aware CNV analysis from single-cell RNA-seq

Generate high quality, publication ready visualizations for single cell transcriptomics data.

Seurat Disk ⭐ 111

Interfaces for HDF5-based Single Cell File Formats

Dynmethods ⭐ 107

A collection of 50+ trajectory inference methods within a common interface 📥📤

Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets

Clustifyr ⭐ 93

Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets

Metacell ⭐ 89

Metacell - Single-cell mRNA Analysis

A tool for unsupervised projection of single cell RNA-seq data

Scimpute ⭐ 58

Accurate and robust imputation of scRNA-seq data

integrated RNA-seq Analysis Pipeline

Dynverse ⭐ 58

A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍

Singlecellexperiment ⭐ 52

Clone of the Bioconductor repository for the SingleCellExperiment package, see https://bioconductor.org/packages/devel/bioc/html/ for the official development version.

Nebulosa ⭐ 50

R package to visualize gene expression data based on weighted kernel density estimation

Cellpypes ⭐ 48

Cell type pipes for R

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

An R-based interface for loom files

R package for pathway analysis in scRNA-seq data

Tidysinglecellexperiment ⭐ 32

Brings SingleCellExperiment objects to the tidyverse

Pipecomp ⭐ 31

A R framework for pipeline benchmarking, with application to single-cell RNAseq

scLearn：Learning for single cell assignment

Plot1cell ⭐ 29

A R package for advanced single cell data viz

Csbb Shiny ⭐ 28

Computational Suite for Bioinformaticians and Biologists (CSBB) is a RShiny application developed with an intention to empower researchers from wet and dry lab to perform downstream Bioinformatics analysis

Seuratv3wizard ⭐ 26

A web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat v3

Commpath ⭐ 24

R toolkit for inference and analysis of pathway-mediated cell-cell communication chain from single-cell transcriptomics

Scisorseqr ⭐ 24

scisorseqr is an R-package for processing of single-cell long read data and analyzing differential isoform expression across any two conditions

Seurat.utils ⭐ 19

Various utility functions for Seurat single-cell analysis

An R package to analyze single-cell V(D)J data

Single-cell Orientation Tracing

Tidygate ⭐ 18

Label elements within user drawn gates

Access and Format Single-cell RNA-seq Datasets from Public Resources

Muto_wilson_ncomm_2020 ⭐ 17

Workflow for analysis of healthy human kidney by snRNAseq and snATACseq

Elefhant ⭐ 17

Ensemble Learning for Harmonization and Annotation of Single Cells (ELeFHAnt) provides an easy to use R package for users to annotate clusters of single cells, harmonize labels across single cell datasets to generate a unified atlas and infer relationship among celltypes between two datasets. It uses an ensemble of three machine learning classifiers 1) RF 2) SVM and 3) LR

An R implementation of the SINCERA pipeline for single cell RNA-seq profiling analysis

single-cell and bulk RNA-seq analyses from counts → pathways → drug candidates.

Splatter Paper ⭐ 15

Data and analysis for the Splatter paper

Toolchest Client Python ⭐ 13

Toolchest Python client

Singlecellworkflow ⭐ 13

Tutorial for the analysis of scRNA-seq data in R

Robustsinglecell ⭐ 13

Robust single cell clustering and comparison of population compositions across tissues and experimental models via similarity analysis.

SCASA: Single cell transcript quantification tool

Seurat Shiny ⭐ 12

Predict cell cycle phase in a continuum from single-cell RNA-seq data

Catd_snakemake ⭐ 11

Snakemake pipeline for benchmarking cell-type deconvolution methods as well as deconvoluting real bulk RNA-seq data with the use of scRNA-seq datasets

Sctreeviz ⭐ 10

R/Bioconductor package to interactively explore single cell clusters at multiple resolutions

Automated ingestion and conversion of various single-cell data formats, within and across species

Wilson_muto_ncomm_2022 ⭐ 8

Containerized workflow for analysis of human diabetic kidney disease by snRNA-seq and snATAC-seq

Testisatlas ⭐ 8

Code used for mouse single cell RNAseq testis atlas

Iteratively Adjusted Surrogate Variable Analysis

Spatially-resolved Transcriptomics via Epitope Anchoring

Access data from the Human Cell Atlas project, directly via R/Bioconductor

Cite Seq_optimization ⭐ 7

Code and results from TotalSeqC antibody titration and pipeline benchmarking for CITE-seq experiments

Clustifyrdatahub ⭐ 7

External single-cell mRNA sequencing data sets for use with clustifyr

Seuratwizard ⭐ 7

This is a web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat.

The CanceR Single Cell ExpressioN Toolkit one-line-command applications.

Ananseseurat ⭐ 6

Single cell ANANSE Gene-regulatory-network analysis from Seurat objects

Characterize A-to-I RNA editing in bulk and single-cell RNA sequencing experiments

Netid_package ⭐ 5

A scalable method to infer fate specific gene regulatory network from single cell gene expression data

A reference-based solution for single-cell analysis

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