ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)

Single-cell Case Control Analysis

Cytometry dATa anALYsis Tools

A tool that allows to get UMI counts from a single cell protein assay

C + python code for pairwise multiple sequence alignment, pulling out this functionality from the Cactus alignment program.

R package for detecting doublets in single-cell RNA sequencing data

Inclusive and efficient quantification of labeling and splicing RNAs for time-resolved metabolic labeling based scRNA-seq experiments

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

SCML Fall 2017 Competition: Can machines learn how the mouse sees?

FREE Divergence Error-Correcting DNA Barcodes

Global, Highly Specific and Fast Filtering of Alignment Seeds

Computational strategy for identifying clonal cells in single-cell CRISPR screen.

High dimensional weighted gene co-expression network analysis

Hardware Acceleration of Long Read Pairwise Overlapping in Genome Sequencing: Open Source Repository

Multi-sample multi-group scRNA-seq analysis tools

Nextflow pipeline for extracting and counting clonal barcodes