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Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST | Nature Communications
Searching large-scale scRNA-seq databases via unbiased cell embedding with Cell BLAST | Nature Communications

scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data | PLOS Computational Biology
scPipe: A flexible R/Bioconductor preprocessing pipeline for single-cell RNA-sequencing data | PLOS Computational Biology

R code and downstream analysis objects for the scRNA-seq atlas of normal and tumorigenic human breast tissue | Scientific Data
R code and downstream analysis objects for the scRNA-seq atlas of normal and tumorigenic human breast tissue | Scientific Data

A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants - ScienceDirect
A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants - ScienceDirect

Longitudinal single-cell RNA-seq analysis reveals stress-promoted chemoresistance in metastatic ovarian cancer | Science Advances
Longitudinal single-cell RNA-seq analysis reveals stress-promoted chemoresistance in metastatic ovarian cancer | Science Advances

Quick start to Harmony • harmony
Quick start to Harmony • harmony

Using R-package scRNAseq (v2.8.0), 52 datasets ranging in date of... | Download Scientific Diagram
Using R-package scRNAseq (v2.8.0), 52 datasets ranging in date of... | Download Scientific Diagram

Single-Cell RNA Sequencing and Assay for Transposase-Accessible Chromatin Using Sequencing Reveals Cellular and Molecular Dynamics of Aortic Aging in Mice | Arteriosclerosis, Thrombosis, and Vascular Biology
Single-Cell RNA Sequencing and Assay for Transposase-Accessible Chromatin Using Sequencing Reveals Cellular and Molecular Dynamics of Aortic Aging in Mice | Arteriosclerosis, Thrombosis, and Vascular Biology

Computational approaches for interpreting scRNA‐seq data - Rostom - 2017 - FEBS Letters - Wiley Online Library
Computational approaches for interpreting scRNA‐seq data - Rostom - 2017 - FEBS Letters - Wiley Online Library

README
README

Genes | Free Full-Text | A Comprehensive Survey of Statistical Approaches for Differential Expression Analysis in Single-Cell RNA Sequencing Studies
Genes | Free Full-Text | A Comprehensive Survey of Statistical Approaches for Differential Expression Analysis in Single-Cell RNA Sequencing Studies

Using R-package scRNAseq (v2.8.0), 52 datasets ranging in date of... | Download Scientific Diagram
Using R-package scRNAseq (v2.8.0), 52 datasets ranging in date of... | Download Scientific Diagram

Single-cell RNA-seq: Pseudobulk differential expression analysis | Introduction to single-cell RNA-seq
Single-cell RNA-seq: Pseudobulk differential expression analysis | Introduction to single-cell RNA-seq

Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis | Nature Communications
Spatiotemporal single-cell RNA sequencing of developing chicken hearts identifies interplay between cellular differentiation and morphogenesis | Nature Communications

Frontiers | A Comparison for Dimensionality Reduction Methods of Single-Cell RNA-seq Data
Frontiers | A Comparison for Dimensionality Reduction Methods of Single-Cell RNA-seq Data

Single-cell RNA sequencing coupled to TCR profiling of large granular lymphocyte leukemia T cells | Nature Communications
Single-cell RNA sequencing coupled to TCR profiling of large granular lymphocyte leukemia T cells | Nature Communications

BingleSeq – a user-friendly R package for bulk and single-cell RNA-Seq data analysis | RNA-Seq Blog
BingleSeq – a user-friendly R package for bulk and single-cell RNA-Seq data analysis | RNA-Seq Blog

Tools for Single Cell Genomics • Seurat
Tools for Single Cell Genomics • Seurat

README
README

BingleSeq: a user-friendly R package for bulk and single-cell RNA-Seq data analysis [PeerJ]
BingleSeq: a user-friendly R package for bulk and single-cell RNA-Seq data analysis [PeerJ]

Single cell RNA sequencing – NGS Analysis
Single cell RNA sequencing – NGS Analysis

Frontiers | Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment
Frontiers | Mapping and Validation of scRNA-Seq-Derived Cell-Cell Communication Networks in the Tumor Microenvironment

CIPR: a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments | BMC Bioinformatics | Full Text
CIPR: a web-based R/shiny app and R package to annotate cell clusters in single cell RNA sequencing experiments | BMC Bioinformatics | Full Text

clustifyr: an R package for automated single-cell... | F1000Research
clustifyr: an R package for automated single-cell... | F1000Research

Deep learning–based cell composition analysis from tissue expression profiles | Science Advances
Deep learning–based cell composition analysis from tissue expression profiles | Science Advances

pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools | Genome Biology | Full Text
pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools | Genome Biology | Full Text

Processing single-cell RNA-seq data for dimension reduction-based analyses using open-source tools - ScienceDirect
Processing single-cell RNA-seq data for dimension reduction-based analyses using open-source tools - ScienceDirect

GitHub - rezakj/iCellR: Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).
GitHub - rezakj/iCellR: Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptomics (ST)).