Overview

This repository contains most of the scripts used to generate figures for

Fansler, M.M., Mitschka, S. & Mayr, C. Quantifying 3′UTR length from scRNA-seq data reveals changes independent of gene expression. Nat Commun 15, 4050 (2024). https://doi.org/10.1038/s41467-024-48254-9

Additional figures were separately generated in the related repositories:

• Human 3' cleavage site analysis: repository (DOI)
• Mouse 3' cleavage site analysis: repository (DOI)
• 3'UTR analysis of Perturb-seq data: repository (DOI)

Organization

The folders in the repository have the following purposes:

• envs - Conda environment YAML files for recreating the execution environment
• figures - source code for generating figures and associated analysis
• metadata - input information used by some scripts
• numbers - source code for generating numbers used in the manuscript
• tables - source code for generating supplementary data and intermediate tables

Input data files to these scripts are deposited to figshare.

Source Code

The primary source code is found in the figures and tables folders. Files are named to correspond with the figures they generate. HTML renders of the RMarkdown files.

Execution Environments

The R instances used to execute the files were captured both in the rendered RMDs themselves (see Runtime Details section in HTMLs) and provided as YAML files in the envs folder.

To recreate on arbitrary platforms (Linux or MacOS), we recommend using Micromamba and the minimal YAML (*.min.yaml):

micromamba create -n bioc_3_16 -f envs/bioc_3_16.min.yaml
micromamba activate bioc_3_16

A fully-solved environment capture is also provided (*.full.yaml). This is only expected to recreate on the osx-64 platform and is primarly intended for exact replication and a statement of record.