kevinrue

# 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

---
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

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

timestamp()
message("Started")

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

kevinrue

---
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

---
title: "Proportion of cells matching signatures"
author: "Kevin Rue-Albrecht"
date: "24/11/2018"
output: html_document
editor_options: 
  chunk_output_type: console
---

```{r setup, include=FALSE}

kevinrue

clonePackageSource <- function(from, to, ignore=c(".git")) {
    unisetRootFiles <- list.files(cloneSourceFolder, all.files = TRUE, include.dirs = TRUE)
    unisetRootFiles <- setdiff(unisetRootFiles, c(".", "..", ".git"))
    dir.create(cloneDestinationFolder, recursive = TRUE)
    for (rootFile in unisetRootFiles) {
        message(rootFile)
        file.copy(
            from = file.path(cloneSourceFolder, rootFile),
            to = file.path(cloneDestinationFolder),
            recursive = TRUE, overwrite = TRUE)

kevinrue

# Introduction -----

timestamp()
message("Started")

# Packages ----

stopifnot(suppressPackageStartupMessages({
    require(optparse)

kevinrue

library(scRNAseq)
data(allen)
class(allen)

# Example data ----

library(scater)
sce <- as(allen, "SingleCellExperiment")
counts(sce) <- assay(sce, "tophat_counts")
sce <- normalize(sce)

kevinrue

#!/bin/bash

original_path=$(pwd)

source_path="/Users/kevin/git/kevinrue.github.io-academic"
site_path="/Users/kevin/git/kevinrue.github.io"

echo_eval () {
  echo "> $1"
  eval "$1"

kevinrue

cloneRepo <- function(from, to) {
    repoFiles <- list.files(cloneSourceFolder, all.files = TRUE, include.dirs = TRUE)
    repoFiles <- setdiff(repoFiles, c(".", "..", ".git"))
    dir.create(to, recursive = TRUE)
    for (rootFile in repoFiles) {
        message(rootFile)
        file.copy(
            from = file.path(from, rootFile),
            to = file.path(to),
            recursive = TRUE, overwrite = TRUE)