hasihays / am_genebasis

prediction of marker genes for cell typing and spatial gradients from scRNA-seq

am_geneBasis

This folder contains scripts to re-generate benchmarking and analysis of geneBasis method for targeted gene panel design (preprint).

Specifically, it contains next folders/scripts:

• functions folder contains scripts with all subfunctions to perform gene search (the package version is available here) as well as additional functions to benchmark the method.
• generateData folder contains scripts to generate data used for this project.
• analysis folder contains scripts to perform analysis for this project.
• scGeneFit folder contains scripts to generate marker selections using method scGeneFit.
• scmer folder contains scripts to generate selections using method SCMER.
• Relevant data including source data and data generated with scripts from generateData can be found on Dropbox: https://www.dropbox.com/sh/sy70359szw982hl/AACXyVsiCKImd2M5q7_Dfhpca?dl=0. Please note, that we have put External data in the subfolder ./External/.

If you have any issues and questions re functions or analysis, please submit an issue on GitHub or contact here: alsu-at-ebi.ac.uk.