Skip to main content

Chemo Genomic Enrichment Analysis

Project description

To use CGEA:
Install: pip install CGEA

CGEA offers two primary classes:
drugListCGEA(druglist, saveAs = "json", sort = 'up', outputDir = None, prefix = 'CGEAResults',
data = {}, numWorkers = cpu_count(), verbose = False, numPermutations = 1000):
geneListCGEA(upgenes, downgenes, saveAs = "json", sort = 'up', outputDir = None, prefix = 'CGEAResults',
data = {}, numWorkers = cpu_count(), verbose = False, numPermutations = 1000):

arguments:
upgenes = list of up regulated genes in your gene set.
downgenes = list of down regulated genes in your gene set. Input None if you don't discriminate between up and down regulation.
druglist = list of drugs in quuery set.
outputDir: if you want to have the function save the outputs for you, supply an output directory here.
prefix: all the file outputs will have this as a prefix if outputDir is defined
async: set this to True if you want the program to run asynchronously
numPermutations: increasing this number will increase accuracy at the cost of speed
verbose: set this to True to have the program give status updates about its progress
numWorkers: how many cores to use
data: you can change what data is used by the program. Advanced users only.

methods:
run - run the process

objects:
results - holds the result data

Example operation:
myUpgenes = [1,2,3]
myDowngenes = [4,5,6]
myCGEA = geneListCGEA(myUpgenes, myDowngenes)
myCGEA.run()
results = myCGEA.results

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for CGEA, version 0.918
Filename, size File type Python version Upload date Hashes
Filename, size CGEA-0.918.tar.gz (32.0 kB) File type Source Python version None Upload date Hashes View hashes

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN DigiCert DigiCert EV certificate StatusPage StatusPage Status page