ryananeff

#!pip install synapseclient
import synapseclient, os
from synapseclient import Project, Folder, File, Link
syn = synapseclient.Synapse()

def upload_files_create_folders(path=".",parent_id=""):
    """ upload_files_create_folders(path=".",parent_id="")
    
    Recursively uploads all files and folders to a Synapse Project or folder.
    

ryananeff

## from: https://github.com/nfusi/qvalue
## edited to work in Python 3 by Ryan Neff, 4/19/18

import scipy as sp
import numpy as np
from scipy import interpolate

def qvalue_estimate(pv, m=None, verbose=False, lowmem=False, pi0=None):
    """
    Estimates q-values from p-values

ryananeff

import numpy as np
import scipy as sp

def acat_test(pvalues,weights=None):
    '''acat_test()
    Aggregated Cauchy Assocaition Test
    A p-value combination method using the Cauchy distribution.
    
    Inspired by: https://github.com/yaowuliu/ACAT/blob/master/R/ACAT.R
    

ryananeff

import numpy as np
import seaborn as sb
import matplotlib.pyplot as plt
import matplotlib as mpl
from matplotlib.collections import PatchCollection

#### heatmap_circle()
##
## Creates a heatmap of values, with size of the circle at a given (row,col) as a second dimension
## uses seaborn's clustermap to provide biclustering

ryananeff

#!/bin/bash

input_file=$1;

if unzip -l "${input_file}" | grep ".tiff"
	then 
		echo "tiffs found, converting..."
		unzip -q "${input_file}" -d test
		for i in test/ppt/media/*.tiff; do sips -s format png "${i}" --out "${i%tiff}png"; rm $i; done
		for i in test/ppt/slides/_rels/*.rels; do echo $i; sed -i -e 's/.tiff/.png/g' $i; done