Christopher L Plaisier, PhD cplaisier
cplaisier
/ oncoMerge_path.py
Last active
August 31, 2020 21:55
— forked from anutua/oncoMerge.py
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| ########################################################## | |
| ## OncoMerge: oncoMerge.py ## | |
| ## ______ ______ __ __ ## | |
| ## /\ __ \ /\ ___\ /\ \/\ \ ## | |
| ## \ \ __ \ \ \___ \ \ \ \_\ \ ## | |
| ## \ \_\ \_\ \/\_____\ \ \_____\ ## | |
| ## \/_/\/_/ \/_____/ \/_____/ ## | |
| ## @Developed by: Plaisier Lab ## | |
| ## (https://plaisierlab.engineering.asu.edu/) ## | |
| ## Arizona State University ## |
cplaisier
/ Correlation Matrix Practice.py
Last active
January 14, 2019 15:14
— forked from mkcook/Correlation Matrix Practice
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| import pandas as pd # May not need this or may have already done this but so you know where pd comes from | |
| #### Two possible solutions | |
| ############################################################################## | |
| ### 1. Calculate all possible values which is what you are doing currently ### | |
| ############################################################################## | |
| corrDF_R = pd.DataFrame(index=df.index, columns=df.index) | |
| corrDF_p = pd.DataFrame(index=df.index, columns=df.index) | |
| for i in corrDF_p.index: |
cplaisier
/ gist:6d644e2064b6e04bb80a14f2258fc489
Last active
November 14, 2018 16:07
— forked from mkcook/gist:6326fe1ea37cb7ab13e6e66a5c80fff3
Practice Computational Task
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| # Import libraries up front | |
| import json | |
| # From Table S13 in Plaisier et al., Cell Systems 2016 | |
| # These are Entrez IDs (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3013746/) | |
| input = ['430', '1052', '1053', '1385', '84699', '9586', '1871', '1874', '144455', '79733', '1960', '1997', '2002', '2004', '80712', '2114', '2115', '2120', '51513', '2551', '2623', '2624', '2625', '9421', '3232', '10320', '3659', '3662', '3670', '91464', '3726', '10661', '11278', '128209', '10365', '9314', '1316', '51176', '9935', '23269', '4602', '4774', '4790', '7025', '9480', '5468', '5914', '5916', '3516', '5971', '864', '6257', '4093', '6659', '6660', '6662', '25803', '347853', '30009', '9496', '6929', '6925', '8463', '7022', '29842', '10155', '6935', '132625', '23051', '85416', '7707', '7764', '23528', '201516'] | |
| # Loading JSON file | |
| # https://www.safaribooksonline.com/library/view/python-cookbook-3rd/9781449357337/ch06s02.html | |
| # Example: |
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
/ const.py
Last active
June 26, 2018 18:04
— forked from ssstrike/NetworkMotifAttributes.py
Updated version.
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| # -*- 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 |
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cplaisier
/ pearsonrGeneExpression.py
Created
May 3, 2018 18:13
— forked from ssstrike/pearsonrGeneExpression.py
input csv of gene expression, creates histogram for p and r values.
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| # -*- coding: utf-8 -*- | |
| """ | |
| Created on Sat Apr 07 21:10:33 2018 | |
| @author: Fuzzy | |
| """ | |
| import math | |
| import pandas as pd | |
| import numpy as np | |
| import matplotlib.pyplot as plt |
cplaisier
/ tf_SubNetworkFunction.py
Last active
April 10, 2018 17:37
— forked from ssstrike/tf_SubNetworkFunction.py
input start gene and hops, output subnetwork.sif
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| # -*- coding: utf-8 -*- | |
| """ | |
| Created on Sat Mar 24 12:19:38 2018 | |
| @author: Fuzzy | |
| """ | |
| import json | |
| with open('tfbsDb_plus_and_minus_5000_entrez.json', 'r') as f: | |
| data = json.load(f) |
cplaisier
/ entrezIDRedundancyRemoval.R
Last active
March 29, 2018 16:02
— forked from oeltoham/Entrez Gene ID Mapping
Script to load up expression data and write out Entrez IDs
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| # Load libraries | |
| library(GEOquery) | |
| library(genefilter) | |
| # Set working directory | |
| setwd('C:/Users/cplaisie/Dropbox (ASU)/ASU/Students/Omar') | |
| # Load up data | |
| gset <- getGEO(filename="data/GSE26253_series_matrix.txt.gz", GSEMatrix=TRUE, AnnotGPL=T) | |
| pData(gset) |
cplaisier
/ TF_TestNetworkFam_3_27_2018.py
Last active
March 27, 2018 17:56
— forked from ssstrike/TF_TestNetwork.py
input network list, dictionary, hops and output full .sif and sub .sif
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| # -*- coding: utf-8 -*- | |
| """ | |
| Created on Sat Mar 24 12:19:38 2018 | |
| @author: Fuzzy | |
| """ | |
| import json | |
| with open('tfbsDb_plus_and_minus_5000_entrez.json', 'r') as f: | |
| data = json.load(f) |
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