armish

armish

armish

armish

#!/bin/bash

set -e

cat helpers/triplets.lst |while read patient
do
	mergedFile=ssms/merged/${patient}.txt
	cat helpers/ssm_header.txt > ${mergedFile}

	count=0

armish

CANCER_IMMUNITY_DIFFERENTIATION_ANTIGENS	http://cancerimmunity.org/peptide/differentiation/	CEACAM5	SILV	SCGB2A2	MLANA	ANKRD30A	GPR143	ACPP	KLK3	RAB38	TYRP1	DCT	TYR
CANCER_IMMUNITY_SHARED_TUMOR_SPECIFIC_ANTIGENS	http://cancerimmunity.org/peptide/tumor-specific/	BAGE	CCNA1	GAGE1	GAGE2A	GAGE8	GAGE3	GAGE4	GAGE5	GAGE6	GAGE7	MGAT5	CXorf61	CCDC110	CTAG2	MAGEA1	MAGEA2	MAGEA3	MAGEA4	MAGEA6	MAGEA9	MAGEA10	MAGEA12	MAGEC1	MAGEC2	MUC1	CTAG1B	SAGE1	SPA17	SSX2	SSX4	CSAG2	DCT	XAGE1B
CANCER_IMMUNITY_ANTIGENS_OVEREXPRESSED_IN_TUMORS	http://cancerimmunity.org/peptide/overexpressed/	PLIN2	LOC51152	ALDH1A1	BCL2L1	WDR46	CALCA	PTPRC	CD274	CPSF1	CCND1	DKK1	ENAH	EPCAM	EPHA3	EZH2	FGF5	GPC3	CA9	ERBB2	HLA-DOB	HPN	IDO1	GPC3	IL13RA2	CES2	AFP	KLK4	KIF20A	CSF1	CSF1	CSPG4	MDM2	MDK	MMP2	MMP7	MUC1	MUC5AC	TP53	PAX5	ZNF395	PRAME	FOLH1	RAGE	RGS5	RhoC	RNF43	DCDC2	SCRN1	SOX10	STEAP1	BIRC5	TERT	TPBG	VEGFA	WT1

armish

/**
 * Visualization of genes, including exons and coding regions.
 * @flow
 */
'use strict';

var React = require('./react-shim'),
    _ = require('underscore'),
    d3 = require('d3'),
    shallowEquals = require('shallow-equals'),

armish

var pileup = require("pileup");

var sources = [
  {
    viz: pileup.viz.genome(),
    isReference: true,
    data: pileup.formats.twoBit({
      url: 'http://www.biodalliance.org/datasets/hg19.2bit'
    }),
    name: 'Reference'

armish

// require() some stuff from npm (like you were using browserify)
// and then hit Run Code to run it on the right

// this doesn't work, because browserify fails due to missing
// transformify dependency
var pileup = require("pileup");

armish

# This function sorts the matrix for better visualization of mutual exclusivity across genes
memoSort <- function(M) {
	geneOrder <- sort(rowSums(M), decreasing=TRUE, index.return=TRUE)$ix;
	scoreCol <- function(x) {
		score <- 0;
		for(i in 1:length(x)) {
			if(x[i]) {
				score <- score + 2^(length(x)-i);
			}
		}

armish

#!/bin/bash

for i in `git ls-files`
do 
        git log --follow -p $i |grep "^commit" |awk "{ print \"$i\tmodified-in\t\" \$2 }"
done