Computational biology, software development, and R package development

Kevin Rue-Albrecht kevinrue

Computational biology, software development, and R package development

Ingénieur diplômé; Computational Biologist; Software engineer; Bioconductor contributor

kevinrue / Seurat_PBMC3k_TENxPBMCData_tutorial.Rmd

Created November 27, 2018 21:51

Seurat - Guided Clustering Tutorial

	---
	title: "Seurat PBMC 3k tutorial using TENxPBMCData"
	author: "Kevin Rue-Albrecht"
	date: "27/11/2018"
	output: html_document
	editor_options:
	chunk_output_type: console
	---

	```{r setup, include=FALSE}

kevinrue / Seurat_PBMC3k_tutorial.R

Created November 25, 2018 18:21

Seurat - Guided Clustering Tutorial


	# Adapted from https://satijalab.org/seurat/pbmc3k_tutorial.html on 2018-11-24

	timestamp()
	message("Started")

	library(BiocFileCache)
	library(Seurat)
	library(dplyr)

kevinrue / Seurat_PBMC3k_proportion_signatures_per_cluster.Rmd

Created November 25, 2018 17:22

Use the signatures declared in the Seurat tutorial to identify the proportion of each cluster positive for each signature.

	---
	title: "Proportion of cells matching signatures"
	author: "Kevin Rue-Albrecht"
	date: "25/11/2018"
	output: html_document
	editor_options:
	chunk_output_type: console
	---

	```{r setup, include=FALSE}

kevinrue / parse_R_dependencies.R

Created October 22, 2018 08:21

Identify the unique list of R packages loaded by "library" or "require" statements

	# The following command:
	# - Parses (recursively) all files within the "R/" folder (Change as relevant).
	# - Identifies all lines that include the statements "require(" or "library(".
	# - Trims everything before and including "require(" or "library(", and everything after the next ")", leaving only the package name.
	# - Identifies the unique list of packages loaded in those ways.

	grep -Rn '.\(require\\|library\)(.' R/* \| sed 's/.\(require\\|library\)(\(.\)).*/\2/g' \| sort \| uniq

kevinrue / newRscript.R

Last active March 26, 2019 14:39

Template for Rscript


	# Introduction -----

	timestamp()
	message("Started")

	# Packages ----

	stopifnot(suppressPackageStartupMessages({
	require(optparse)