Bruno Grande BrunoGrandePhD

Senior Software Engineer. Advocate for open and reproducible science. Certified Carpentries and RStudio Tidyverse trainer. Nature and wildlife photographer.

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BrunoGrandePhD / multi-gather.md

Last active July 20, 2018 01:29

Gather (melt) on multiple columns at once

library(data.table)
library(tidyverse)

anscombe

#>    x1 x2 x3 x4    y1   y2    y3    y4
#> 1  10 10 10  8  8.04 9.14  7.46  6.58
#> 2   8  8  8  8  6.95 8.14  6.77  5.76
#> 3  13 13 13  8  7.58 8.74 12.74  7.71

BrunoGrandePhD / template.html

Created January 11, 2018 20:11

	<html>
	<head>
	<title>Unix Lab Web Page Example</title>
	<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
	<meta name="keywords" content="Bioinformatics, Fiona Brinkman, course">
	<meta name="description" content="This is a template file to help you learn about HTML.">
	</head>

	<body bgcolor="#FFFFFF" text="#000000">
	<p><b><font size="+2" color="#0000FF">

BrunoGrandePhD / restdata.csv

Created October 4, 2017 17:08

gender	eat_out	weight
F	0	110
F	0	114
F	0	115
F	0	110
F	0	125
F	0	140
F	0	130
F	0	145
F	0	158

BrunoGrandePhD / Dockerfile

Created January 31, 2017 02:01

"Sentiment Analysis for Amazon Product Reviews" by Apala Guha

	FROM ubuntu:latest
	RUN apt-get update
	RUN apt-get install -y vim wget git htop tmux
	RUN apt-get install -y openssh-client default-jre default-jdk
	RUN apt-get install -y python2.7
	RUN ln -s /usr/bin/python2.7 /usr/bin/python
	RUN wget https://bootstrap.pypa.io/get-pip.py
	RUN python get-pip.py
	RUN pip2.7 install numpy
	RUN pip2.7 install pandas

BrunoGrandePhD / remove-big-file.sh

Created December 15, 2016 01:16

Remove a large committed file from your Git repository.

-# The commands below are a guide to remove a large file that has been
-# accidentally committed to a Git repository's history. If the file is
-# larger than 100 MB, GitHub will prevent you from pushing your latest
-# commits. The annotated steps below should help you remove the large
-# file from your commit history, even if you've made new commit since.
-# Some Git users advise against rebasing. You can safely use it here
-# because you haven't published your changes yet.
-# So, you first need to rebase your current branch onto the point that

BrunoGrandePhD / ggplot2_workshop.R

Created October 26, 2016 00:03

R script capturing what was covered in the SciProg.ca workshop on ggplot2 (https://github.com/sciprog-sfu/sciprog-sfu.github.io/issues/143)

	## GGplot2 workshop Sciprog October 24 2016
	# Author: Michelle Jones

	library(ggplot2)
	#install the packages for the workshop
	#install.packages(c("tidyverse","ggthemes","cowplot"))
	#install.packages("gapminder")
	#Load packages
	library(tidyverse)
	library(ggthemes)

BrunoGrandePhD / switch-master.sh

Last active August 18, 2016 14:38

Solution for https://twitter.com/genetics_blog/status/766267301796704256

	git branch new-master # Assumption: HEAD is pointing to the new commits
	git checkout master
	git branch before-revert
	git revert --no-edit commit_X..master # Revert the commits you want to discard
	git rebase -i before-revert # Optional: squash all commits except top one to create one revert commit
	git checkout new-master
	git rebase master
	git checkout master
	git merge new-master
	git branch -D new-master before-revert

BrunoGrandePhD / calc_exon_cov.sh

Last active June 22, 2016 18:13

Command for calculating average coverage for genes in a targeted sequencing experiment

	# Input:
	# - exons.bed: Exons BED file with the fourth column containing the gene name for gene coverage summarizing
	# - sample.bam: BAM file using the same genome build (aka chromosome names and coordinate system) as exons.bed
	# Output:
	# - Tab-delimited file with two columns: gene name and average coverage

	samtools bedcov exons.bed sample.bam \
	\| awk ' \
	BEGIN { \
	FS=OFS="\t"} \

BrunoGrandePhD / fixpdf.sh

Created June 19, 2016 23:53

Sometimes, the font is messed up on a printed version of a PDF file. It seems that this may be caused by the missing embedded fonts in the PDF file. The following shell function simplifies the process.

	# Ensure that fonts are embedded in a PDF file for correct printing
	# Credit: http://stackoverflow.com/a/4234150
	function fixpdf {
	# Print usage is no arguments are given
	if [ "$#" -eq 0 ]; then
	echo "Usage: fixpdf PDF_FILE [PDF_FILE ...]"
	fi
	# Check if ghostscript is installed
	if ! type gs >/dev/null 2>&1; then
	echo 'Error: ghostscript is either not installed or not in your PATH.'

BrunoGrandePhD / icgc_to_maf.R

Created June 16, 2016 23:14

A simple R script to convert an ICGC simple mutations file into the TCGA MAF format for re-annotation with maf2maf (see vcf2maf)

	suppressPackageStartupMessages({
	library(readr)
	library(dplyr)
	})

	maf_cols <- c(
	"Hugo_Symbol","Entrez_Gene_Id","Center","NCBI_Build","Chromosome","Start_Position",
	"End_Position","Strand","Variant_Classification","Variant_Type","Reference_Allele",
	"Tumor_Seq_Allele1","Tumor_Seq_Allele2","dbSNP_RS","dbSNP_Val_Status","Tumor_Sample_Barcode",
	"Matched_Norm_Sample_Barcode","Match_Norm_Seq_Allele1","Match_Norm_Seq_Allele2",

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