A tool for semi-automatic cell type classification

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)).

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.

Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

CellNet: network biology applied to stem cell engineering

scPretrain: Multi-task self-supervised learning for cell type classification

singleCellNet in Python

scoreCT: Automated Cell Type Annotation

Unbiased single-cell transcriptomic data cell type identification

The source code and results for different methods on annotating external testing datsets of human and mouse.

Supervised cell type identification for scATAC-seq data

The official implementation for "SANGO".

CimpleG, an R package to find (small) CpG signatures.

A pipeline to predict risk genes, implicated cell types and drugs for repurposing based on known risk genes (derived from GWAS) for complex traits.

Pipeline for consensus prediction of cell types in single-cell RNA sequencing data.

GUI for semi-automatic single neuron classification by cell type

Annotation and Analysis of Multiplexed Imaging Data

An R package for cell type nomenclature

A Flask app for the Vickaryous & Hall 2006 cell type classification