tiagochst

# ---------------------------
# Accessing the material
# https://tinyurl.com/bioc2017-ELMER
# ---------------------------
library("Bioc2017.TCGAbiolinks.ELMER")
Biobase::openVignette("Bioc2017.TCGAbiolinks.ELMER")

# ---------------------------
# Section 1: 
# Aims:

seandavi

ckandoth

Ensembl's VEP (Variant Effect Predictor) is popular for how it picks a single effect per gene as detailed here, its CLIA-compliant HGVS variant format, and Sequence Ontology nomenclature for variant effects.

To follow these instructions, we'll assume you have these packaged essentials installed:

## For Debian/Ubuntu system admins ##
sudo apt-get install -y build-essential git libncurses-dev

## For RHEL/CentOS system admins ##
sudo yum groupinstall -y 'Development Tools'
sudo yum install -y git ncurses-devel

ShixiangWang

#---------------------------------------------------
# Filter TCGA Replicate Samples
# Author: ShixiangWang <[email protected]>
# ooooooo
# The filter rule following broad institute says:
#
# In many instances there is more than one aliquot for a given combination of individual, platform, and data type. However, only one aliquot may be ingested into Firehose. Therefore, a set of precedence rules are applied to select the most scientifically advantageous one among them. Two filters are applied to achieve this aim: an Analyte Replicate Filter and a Sort Replicate Filter.
# 
# Analyte Replicate Filter
# The following precedence rules are applied when the aliquots have differing analytes. For RNA aliquots, T analytes are dropped in preference to H and R analytes, since T is the inferior extraction protocol. If H and R are encountered, H is the chosen analyte. This is somewhat arbitrary and subject to change, since it is not clear at present whether H or R is the better protocol. If there are multiple aliquots as

grst

#!/bin/bash
USER=`whoami`
source /etc/profile

# Source global definitions
if [ -f /etc/bashrc ]; then
  . /etc/bashrc
fi

source /storage/apps/dotfiles/bashrc.sh

jasonsychau

# a combination of
# https://stackoverflow.com/questions/1815606/determine-path-of-the-executing-script/15373917#15373917
# https://stackoverflow.com/questions/1815606/determine-path-of-the-executing-script/7585599#7585599
# https://stackoverflow.com/questions/47044068/get-the-path-of-current-script/47045368#47045368
# https://stackoverflow.com/questions/53512868/how-to-automatically-include-filepath-in-r-markdown-document/53516876#53516876
stub <- function() {}
thisPath <- function() {
  cmdArgs <- commandArgs(trailingOnly = FALSE)
  if (length(grep("^-f$", cmdArgs)) > 0) {
    # R console option