Compound Pearson residuals for single-cell RNA-seq data without UMIs

This repository holds the code needed to reproduce the analyses and figures presented in our preprint Lause et al. (2023), including additional analysis that was requested during peer review for a journal submission. The code for the earlier version of the preprint can be found under earlier releases (v1, v2). Code release v1 corresponds to v1 of the preprint, code release v2 to the current version of the preprint. Release v3.0 contains the most recent revision analyses.

Code

Some of the notebooks and R scripts depend on each other and are best run in the order indicated. For the R scripts, use our separate R environment (see below for setup instructions). Notebooks/Scripts 1-18 use the Tasic 2018 dataset. Notebooks 19-24 are based on the reads-per-UMI tables from the Ziegenhain/Hagemann-Jensen datasets.

Datasets

• Download the reads-per-UMI tables from zenodo and save them to .data/reads_per_umi_tables/. R code to obtain the same tables from the public raw data is available in data/reads_per_umi_tables/prepare_data.R.
• Download the Tasic raw count data from brain-map.org via the Gene-level (exonic and intronic) read count values for all samples (zip) link. From these *.zip files, extract the mouse_ALM_2018-06-14_exon-matrix.csv and mouse_VISp_2018-06-14_exon-matrix.csv to .data/tasic/.
• All required metadata tables are contained in this repository for convenience.

Compute environment

We ran all notebooks in Python 3.8.10 on an Ubuntu machine with 40 CPUs and 440 GB RAM. The following package versions were used:

• scanpy 1.9.0
• anndata 0.8.0
• sklearn 1.0.2
• numpy 1.21.5
• matplotlib 3.5.1
• openTSNE 0.6.0
• pandas 1.4.1
• seaborn 0.11.2
• mygene 3.2.2.
• scipy 1.8.0

Census and qUMI where run in a separate R conda environment specified in r41_env.yml. To install it, create the environment from that file with

conda env create -f r41_env.yml

Then, to install qUMI, activate the environment with conda activate r41_env_full, start R and run

remotes::install_github("willtownes/quminorm")