Ming Tang crazyhottommy

library('TCGAbiolinks')
library('plyr')
library('devtools')

projects<- "TCGA-LUAD"

clin &lt;- lapply(projects, function(p) {

save the below script to convert_gmt_perline.sh:

This function translate the human gene symbol to mouse gene symbol for each line.

I downloaded the manifest file from gdc, but it only has the uuid, I will need to convert them to TCGA barcode.

A function from the link above

library(httr)

and I want to create a super-set of EP interaction across all cell lines. It turns out to be not that easy...

#only for encode and roadmap data
mkdir Encoderoadmap_EP_interaction

ssh mdaris337
conda create -n R330

source activate R330

conda install -c r r=3.3.2 r-essentials

	#install UMAP from https://github.com/lmcinnes/umap
	#install.packages("rPython")

	umap <- function(x,n_neighbors=10,min_dist=0.1,metric="euclidean"){
	x <- as.matrix(x)
	colnames(x) <- NULL
	rPython::python.exec( c( "def umap(data,n,mdist,metric):",
	"\timport umap" ,
	"\timport numpy",
	"\tembedding = umap.UMAP(n_neighbors=n,min_dist=mdist,metric=metric).fit_transform(data)",

	Gene ID Transcript ID Human associated gene name Human gene stable ID Associated Gene Name
	ENSMUSG00000064336 ENSMUST00000082387 mt-Tf
	ENSMUSG00000064337 ENSMUST00000082388 mt-Rnr1
	ENSMUSG00000064338 ENSMUST00000082389 mt-Tv
	ENSMUSG00000064339 ENSMUST00000082390 mt-Rnr2
	ENSMUSG00000064340 ENSMUST00000082391 mt-Tl1
	ENSMUSG00000064341 ENSMUST00000082392 MT-ND1 ENSG00000198888 mt-Nd1
	ENSMUSG00000064342 ENSMUST00000082393 mt-Ti
	ENSMUSG00000064343 ENSMUST00000082394 mt-Tq
	ENSMUSG00000064344 ENSMUST00000082395 mt-Tm

	#! /bin/bash
	set -e
	set -u
	set -o pipefail

	root=`pwd`

	mkdir macs14_pbs

	cat bam_names.txt \| while read -r IP Input

	---
	title: "02_bioc_curated_TCGA_data"
	author: "Ming Tang"
	date: "November 9, 2017"
	output: html_document
	---

	```{r}
	devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")
	library(here)

	#!/bin/bash

	printf "\n * BIS BATCH PRIMER version 2.0 *"
	printf "\n\n !!! 'Primer3 & fastx-toolkit' must be installed on the system.\n\n !!! Edit parameters (e.g. sizes, Tm, and etc) before start\n\n "
	printf "\n\n Usage : \n ./mp_primer.sh FASTA PARAMETER \n\n"
	printf " >>> input FASTA = "$1
	printf " \n >>> parameters = "$2
	printf "\n\n\n ()()() Running... \n\n"

	if [ -f $1 -a -f $2 ]; then