Christopher L Plaisier, PhD cplaisier

Associate Professor, School of Biological and Health Systems Engineering Arizona State University Temp, Arizona

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cplaisier / ConvertGS2Entrez_postProc.py

Created September 18, 2018 05:03

Coverts postProcessed files to have entrez IDs.

	import csv
	import pandas as pd

	gene2entrez = []
	with open('gene2entrez.csv', mode='r') as infile:
	reader1 = csv.reader(infile)
	gene2entrez = {row1[0]:row1[1] for row1 in reader1}

	for post in ['pita','targetscan','tfbs_db']:
	# read in the gene symbol map and the post proc

cplaisier / plotNetworkMotifs_V2heatmap_byGrade.py

Created August 13, 2018 21:16

Look at lines 29, 30, 263-280, 342-353, 371-382

	##########################################################
	## Consistilator: plotNetworkMotifs.py ##
	## ______ ______ __ __ ##
	## /\ __ \ /\ ___\ /\ \/\ \ ##
	## \ \ __ \ \ \___ \ \ \ \_\ \ ##
	## \ \_\ \_\ \/\_____\ \ \_____\ ##
	## \/_/\/_/ \/_____/ \/_____/ ##
	## @Developed by: Plaisier Lab ##
	## (https://plaisierlab.engineering.asu.edu/) ##
	## Arizona State University ##

cplaisier / replicationDatasetPermutation.R

Created August 1, 2018 15:17

Newer version of replication.

	#!/usr/bin/env Rscript

	suppressMessages(library(WGCNA))
	suppressMessages(library(multicore))
	suppressMessages(library(getopt))
	suppressMessages(library(parallel))
	suppressMessages(library(impute))
	suppressMessages(library(survival))

	# read command line arguments

cplaisier / 5.16.18.Final.py

Created July 25, 2018 17:56

Ethan's Code

	# Loading JSON file
	# https://www.safaribooksonline.com/library/view/python-cookbook-3rd/9781449357337/ch06s02.html
	# Example:
	# import json
	#
	# # Reading data back
	# with open('data.json', 'r') as f:
	# data = json.load(f)

	import json

cplaisier / network.py

Created July 10, 2018 19:24

Had to modify the 'network.py' file from the BooleanNet python package to get this to work. Needed to be modified to allow components to be imported instead of component. And also to get all strongly connected components produces a generator, which needed to be turned into a list.

	import util
	import random
	from itertools import count

	try:
	import networkx
	from networkx import components
	except ImportError:
	util.error( "networkx is missing, install it from https://networkx.lanl.gov/")

cplaisier / task 1 part 2.ipynb

Last active July 25, 2018 15:48 — forked from Dbyrum/task1part2.ipynb

adding a new file to the task in order to pull new information and create another network

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cplaisier / plotNetworkMotifs.py

Created July 2, 2018 19:28

With survival analysis and network states.

	##########################################################
	## Consistilator: plotNetworkMotifs.py ##
	## ______ ______ __ __ ##
	## /\ __ \ /\ ___\ /\ \/\ \ ##
	## \ \ __ \ \ \___ \ \ \ \_\ \ ##
	## \ \_\ \_\ \/\_____\ \ \_____\ ##
	## \/_/\/_/ \/_____/ \/_____/ ##
	## @Developed by: Plaisier Lab ##
	## (https://plaisierlab.engineering.asu.edu/) ##
	## Arizona State University ##

cplaisier / const.py

Last active June 26, 2018 18:04 — forked from ssstrike/NetworkMotifAttributes.py

Updated version.

	# -- coding: utf-8 --
	"""
	Created on Mon Jun 18 21:14:50 2018

	@author: Fuzzy
	"""

	import numpy as np
	import pandas as pd
	import networkx as nx

cplaisier / task1.ipynb

Created June 11, 2018 20:07 — forked from Dbyrum/task1.ipynb

first task

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cplaisier / consistilatorV2.py

Created June 5, 2018 18:56

Code to do consistency checking and plotting of network motifs.

	##########################################################
	## Consistilator: consistilatorV2.py ##
	## ______ ______ __ __ ##
	## /\ __ \ /\ ___\ /\ \/\ \ ##
	## \ \ __ \ \ \___ \ \ \ \_\ \ ##
	## \ \_\ \_\ \/\_____\ \ \_____\ ##
	## \/_/\/_/ \/_____/ \/_____/ ##
	## @Developed by: Plaisier Lab ##
	## (https://plaisierlab.engineering.asu.edu/) ##
	## Arizona State University ##

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