Skip to content

An automated web search for human antibodies labelling neurons and glia in the brain. Takes the direct output of Seurat's "FindMarkers()" and returns a data frame of antibodies based on information from the human protein atlas.

License

Notifications You must be signed in to change notification settings

kaitsull/proteinsearch

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

3 Commits
 
 
 
 
 
 

Repository files navigation

proteinsearch.py

An automated web search for human antibodies labelling neurons and glia in the brain.
This code takes the direct output of Seurat's FindMarkers() and returns a data frame of antibodies based on information from the human protein atlas.

Instructions:

  1. Save a .csv of the marker genes for your single cell RNA sequencing data: write.csv(FindMarkers(data), markers.csv)
  2. In your terminal, ensure that Selenium web driver is installed: pip install selenium
  3. Download Chrome driver here.
  4. In the terminal, navigate to the directory holding proteinsearch.py.
  5. In the terminal, type: python proteinsearch.py
  6. Enter the absolute path of your marker gene csv.
  7. Enter the name of of the output file (be sure to include .csv at the end).
  8. Chrome driver will open and begin the search!

About

An automated web search for human antibodies labelling neurons and glia in the brain. Takes the direct output of Seurat's "FindMarkers()" and returns a data frame of antibodies based on information from the human protein atlas.

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published

Languages