spapros_reproducibility

This repository contains the code to reproduce the analyses and figures of the manuscript "Probeset selection for targeted spatial transcriptomics". The manuscript is currently under review. Preprint at bioRxiv.

The repository is structured as follows:

• preprint folder: contains the scripts and notebooks to reproduce the analyses and figures till the preprint version. This includes Figures 1c, 2c,d,e 3, S1, S2a, S3, S4, S5, S6, S7, S9b,c.
• revision folder: contains the scripts and notebooks to reproduce the analyses and figures for the revised version of the manuscript. This includes Figures 4, S2b, S8, S9a, S10, S11, S12, S13.
• For the revised version we ran extensive benchmarks with our snakemake pipeline (release tag 0.1.0). The configurations for rerunning the experiments can be found there at spapros-smk/configs/ with the file names config_rev.yaml, config_rev_bm.yaml, config_rev_bm_probes.yaml.

Please do not hesitate to open an issue in case of any questions or issues.