Shawn Striker ssstrike
ssstrike
/ TfCascade.py
Last active
September 13, 2018 19:46
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| import json | |
| import pandas as pd | |
| from scipy.stats import pearsonr | |
| # Make a Biotapestry CSV file | |
| def biotapestry(filename, data, regions): | |
| writeMe = [] | |
| writeMe.append('"# Model Commands",,,,,,,,,,') | |
| writeMe.append('"# Command Type","Model Name","Parent Model",,,,,,,,') | |
| writeMe.append('"model","root",,,,,,,,,') |
ssstrike
/ NetworkMotifAttributes.py
Last active
July 24, 2018 16:00
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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 |
ssstrike
/ pearsonrGeneExpression.py
Last active
May 22, 2018 15:39
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 |
ssstrike
/ pandasPTest
Created
April 10, 2018 05:07
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| # -*- coding: utf-8 -*- | |
| """ | |
| Created on Sat Apr 07 21:10:33 2018 | |
| @author: Fuzzy | |
| """ | |
| import pandas as pd | |
| #import numpy as np |
ssstrike
/ tf_SubNetworkFunction.py
Created
April 3, 2018 06:31
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) |
ssstrike
/ TF_TestNetwork.py
Last active
April 10, 2018 05:06
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 pandas as pd | |
| import json | |
| with open('tfbsDb_plus_and_minus_5000_entrez.json', 'r') as f: | |
| data = json.load(f) |
ssstrike
/ TF_NetworkEntrez.py
Last active
March 20, 2018 17:31
takes an input Entrez ID and outputs a .sif file
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| # -*- coding: utf-8 -*- | |
| """ | |
| Created on Mon Mar 12 18:16:24 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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| # -*- coding: utf-8 -*- | |
| """ | |
| Created on Mon Mar 12 18:16:24 2018 | |
| @author: Fuzzy | |
| """ | |
| import json | |
| with open('tfbsDb_plus_and_minus_5000_entrez.json', 'r') as f: | |
| data = json.load(f) |
ssstrike
/ TF_TestNetwork.py
Created
March 12, 2018 04:00
Outputs list of associated Entrez ID to an input Entrez ID
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| """ | |
| Created on Sun Mar 04 18:25:32 2018 | |
| @author: Fuzzy | |
| """ | |
| import json | |
| with open('tfbsDb_plus_and_minus_5000_entrez.json', 'r') as f: | |
| data = json.load(f) |