Skip to content

Automated tool for single-cell cluster annotation running on the fGSEA framework

License

Notifications You must be signed in to change notification settings

alex-trapp/sc-fgsea

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

16 Commits
 
 
 
 
 
 
 
 
 
 
 
 

Repository files navigation

sc-fgsea

sc-fgsea performs cluster annotation of single-cell RNA sequencing data. The tool runs on the fGSEA framework and leverages existing cell-type specific genesets to enable itterative, supervised annotation based on computed p-values and enrichment scores.

The documented code for sc-fgsea is provided as an R markdown file, which can easily be loaded into RStudio.

This tool was developed by Alexandre Trapp in the context of Emmrich et al (2022):

Characterization of naked mole-rat hematopoiesis reveals unique stem and progenitor cell patterns and neotenic traits
Stephan Emmrich, Alexandre Trapp, Frances Tolibzoda Zakusilo, Maggie E Straight, Albert K Ying, Alexander Tyshkovskiy,
Marco Mariotti, Spencer Gray, Zhihui Zhang, Michael G Drage, Masaki Takasugi, Jan-Henning Klusmann, Vadim N Gladyshev,
Andrei Seluanov, Vera Gorbunova

Input

Required data files (located in the data folder) are also provided to run the tool and reproduce the analysis.

The input to sc-fgsea consists of two components:

Example markers and atlas files are provided in data:

  • atlasV14.gmt
  • hglBM.NOmp.markers.clust.txt

Output

The output of sc-fgsea is an Excel file, containing p-values and enrichment scores for each geneset/cluster pair from the input marker file and atlas. An example output file (hglBM.cluster.markers.output.xlsx) can be found in the output folder, with the following format:

pathway pval padj ES NES nMoreExtreme size leadingEdge cluster
ROSSI_mLTHSC 0.009482058 0.039587592 -0.854460094 -1.738297467 384 3 CALML4, UPP1, CLU 1

About

Automated tool for single-cell cluster annotation running on the fGSEA framework

Topics

Resources

License

Stars

Watchers

Forks