willtownes / quminorm-paper

supporting code for the quasi-UMIs single-cell RNA-seq paper
GNU Lesser General Public License v3.0
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Quantile normalization of single-cell RNA-seq read counts without unique molecular identifiers

DOI

This repository contains supporting code to facilitate reproducible analysis. For details see the biorxiv preprint. If you find bugs please create a github issue.

The quasi-UMI normalization method is under development as a standalone R package.

The purpose of this method is to remove PCR distortion from scRNA-seq read counts by normalizing to quasi-UMIs (QUMIs). QUMIs approximate the true (unmeasured) UMI counts. Once read counts are transformed to QUMIs, the count matrix can be passed to UMI-specific methods for feature selection and dimension reduction.

Authors

Will Townes and Rafael Irizarry

Description of Repository Contents

algs

Implementation of quasi-UMI normalization methods, auxiliary functions, and methods used in comparisons.

qumi

Code for making graphs that involved multiple datasets.

real

Analysis of various real scRNA-seq datasets. The Rmarkdown files can be used to produce figures in the manuscript. The util subfolder contains numerous scripts for generating count matrices from FASTQ files, working with BUS files, and running QUMI normalization on large matrices using parallelization on a high performance computing cluster.

util

Miscellaneous utility functions.