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

scplotter is an R package that is built upon plotthis. It provides a set of functions to visualize single-cell sequencing and spatial data in an easy and efficient way.

A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools

Brings SingleCellExperiment objects to the tidyverse

Joint Trajectory Inference for Single-cell Genomics Using Deep Learning with a Mixture Prior

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

Tool for modelling of mitochondrial heteroplasmy

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

This package has migrated to https://github.com/rezakj/iCellR please use iCellR instead of scSeqR for more functionalities and updates.

Supplementary information to "Computational correction of index switching in multiplexed sequencing libraries" (Larsson et. al 2018).

resVAE is a restricted latent variational autoencoder that we wrote to uncover hidden structures in gene expression data, especially using single-cell RNA sequencing. In principle it can be used with any hierarchically structured data though, so feel free to play around with it.

Script for my thesis of single cell rna seq

A command-line utility, a la samtools, that helps to manage and manipulate single-cell data files

(NOTE: This is a development fork, please refer to official repo at statgen: https://github.com/statgen/popscle) Freemuxlet methods and auxilary tools

A computational approach tool to predict Head and Neck Cancer affected patients from their single cell RNA seq data.

SCarborSNV is an efficient algorithm for phylogeny aware genotyping of single cell genomes, using dynamic programming and neighbor joining.

Single-Cell Data Science