Clustering scRNAseq by genotypes

scGNN (single cell graph neural networks) for single cell clustering and imputation using graph neural networks

Quantifying experimental perturbations at single cell resolution

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

Single cell type annotation guided by cell atlases, with freedom to be queer

scRNA multimodal analysis pipeline utilised for large dataset processing

Single cell analysis using Low Resource

orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.

Folded and map strategy and cell perturbation response prediction

AutoML-based Genetic regulatory Element extrAction System

scSPARKL is an Apache spark based pipeline for performing variety of preprocessing and downstream analysis of scRNA-seq data.

PyPairs - A python scRNA-Seq classifier

M2ASDA

PHet: Heterogeneity-Preserving Discriminative Feature Selection for Subtype Discovery

Finding and analyzing alternate poly-A sites in 3' scRNA-seq 10X files

Tools, wrappers, utilities, and resources for handling single-cell and spatial transcriptomics data

An effective tool for single-cell RNA sequencing.

Constructing a developmental tree from scRNA-seq data

Iteratively randomly pooling scRNA-seq expressing a given gene from different numbers of cells and running DESeq2 with fdrtools correction to determine how many times which genes come out as enriched with said gene