Tools

 

scEP

 

single-cell expression prediction (scEP) is a method to predict cell-type specific expression from promoter sequences.
code | preprint

 

treeArches

 

treeArches is a method to build atlases from annotated single-cell RNA-seq datasets which allows continuous addition of new (un)annotated datasets. treeArches is part of the scArches repository.
tutorial | preprint

 

TopoGAN

 

TopoGAN is a method to perform diagonal alignment of single-cell data with unmatched cells and features.
code | preprint

 

scMoC

 

scMoC is amethod to co-cluster multimodal single-cell data (mRNA+ATAC).
code | paper

 

DDA

 

DDA is an R package to perform Differential Dropout Analysis to identify genes with significantly different number of zeros across biological conditions.
code | wed portal | paper

 

scHPL

 

single-cell Hierarchical Progressive Learning method (scHPL) automatically finds relationships between populations of cells across datasets and uses this to construct a classification tree.
code | paper

 

SpaGE

 

A method to predict whole-transcriptome expression of spatial transcriptomics data through integration with scRNA-seq data.
code | paper

 

Cytosplore-Transcriptomics

 

A standalone application for interactive visualization and analysis of large single-cell RNA sequencing data.
software | preprint

 

SCHNEL

 

A highly scalable method to cluster single-cell data (CyTOF and scRNA-seq) with millions of cells.
SCHNELpy | SCHNELr | paper

 

single-cell classification benchmark workflow

 

A Snakemake workflow to benchmark scRNA-seq classifiers. The workflow supports future extension with new classifiers and datasets.
code | paper

 

Pancreas Cell Atlas

 

RShiny app to visualize a comprehensive pancreatic cell atlas created by integrating seven publicly available scRNA-seq pancreatic datasets.
software

 

Cytosplore Viewer

 

An interactive visual analysis system for the exploration of single cell data published in the Allen Cell Types Database and for a number of the single cell data resources of the Brain Initiative Single Cell Network (BICCN).
software | paper | video: intro | video: use case

 

CyTOF linear classifier

 

An LDA classifier to automatically method to annotate cells in CyTOF dataset.
code | paper

 

CyTOFmerge

 

A method to integrate CyTOF data measured from the same biological sample on different panels.
code | paper

 

BrainScope

 

An interactive webtool to visualize brain gene expression data from the Allen Human Brain Atlas and the BrainSpan Atlas of the developing human brain.
software | paper | tutorial video