Ming Tang crazyhottommy

use diffbind to get diff sites

library(DiffBind)
UCI.H3K27ac.dba<- dba(sampleSheet="H3K27ac_diffbind.csv", scoreCol= 7, filter=80, peakFormat = "macs")

UCI_H3K27ac_RPKM<- dba.count(UCI.H3K27ac.dba, minOverlap=2, 
                      fragmentSize = 200, bParallel = T,
                      score = DBA_SCORE_RPKM)

backup dotfiles

Following will copy all of dot ~/. files and directories (including its contents) directly underneath home directory.
To avoid copying cache and other local configs, e.g., that of web browser, java apps, etc., preferably query directory size tool under entire home $HOME/, using ncdu $HOME of similar tool.
Exclude all those large directories using rsync --exclude=.local --exclude=.cache format
Avoid rsync password, ssh keys, .bash_history, etc. if you are uploading to github, etc.
rsync home dotfiles and configs as follows:

# in your local machine

library(tidyverse)

## read in the mutect files
mix.files<- as.list(dir(".", pattern= "*.tsv"))

## need to add the file name into a column
mix_mutect_datlist <- lapply(mix.files, function(f) {
        dat = read.table(f, header =T, sep ="\t", quote = "\"")

colors = structure(circlize::rand_color(4), names = c("a", "b", "c", "d"))
discrete_mat = matrix(sample(letters[1:4], 100, replace = TRUE), 10, 10)



cell_fun = function(j, i, x, y, width, height, fill) {
	grid.rect(x = x *0.6, y = y, width = width * 0.6, height = height, 
		gp = gpar(col = "grey", fill = fill))
}

Pathway analysis using GREAT

rGREAT is an R client written by the same author of ComplexHeatmap for the web GREAT Tool


#library(devtools)
#install_github("jokergoo/rGREAT")
library(rGREAT)

From David Robinson:

A tidyverse approach to ROC curves #rstats pic.twitter.com/buizc7U9ns
— David Robinson (@drob) November 29, 2016

library(tidyverse)
theme_set(theme_minimal())

export VEP_PATH=$HOME/vep
export VEP_DATA=$HOME/.vep

mkdir $VEP_PATH $VEP_DATA; cd $VEP_PATH
curl -LO https://github.com/Ensembl/ensembl-tools/archive/release/86.tar.gz
/usr/local/Cellar/gnu-tar/1.29_1/bin/tar -zxf 86.tar.gz --starting-file variant_effect_predictor --transform='s|.*/|./|g'

rsync -zvh rsync://ftp.ensembl.org/ensembl/pub/release-86/variation/VEP/homo_sapiens_vep_86_GRCh37.tar.gz $VEP_DATA

	query.maf.hg19 <- GDCquery(project = "TCGA-COAD",
	data.category = "Simple nucleotide variation",
	data.type = "Simple somatic mutation",
	access = "open",
	legacy = TRUE)
	# Check maf availables
	knitr::kable(getResults(query.maf.hg19)[,c("created_datetime","file_name")])

	query.maf.hg19 <- GDCquery(project = "TCGA-COAD",
	data.category = "Simple nucleotide variation",

	#!/bin/bash

	# Script for installing tmux on systems where you don't have root access.
	# tmux will be installed in $HOME/local/bin.
	# It's assumed that wget and a C/C++ compiler are installed.
	# original from https://gist.github.com/smsharma/0003b61a571cab63ad80

	# exit on error
	set -e

	#!/bin/sh

	## orginal from https://gist.github.com/lazywei/12bc1669dc7739dccef1
	## author Ming Tang (Tommy)
	## 2016-11-20

	set -e
	set -u
	set -o pipefail