arraytools’s gists

arraytools / simulation_logrank_test.R

Created December 2, 2024 21:55

Compare the effects of sample size on the log-rank test

	library(survival)

	# Function to generate survival data
	generate_data <- function(sample_size, event_rate_group1, event_rate_group2) {
	group <- c(rep(1, sample_size), rep(0, sample_size))
	event_times <- c(rexp(sample_size, rate = event_rate_group1),
	rexp(sample_size, rate = event_rate_group2))
	observed <- rep(1, sample_size * 2) # Assuming all events are observed
	data <- data.frame(group = group, event_times = event_times, observed = observed)
	return(data)

arraytools / Singularity

Last active April 20, 2024 12:05

Corrected singularity definition file for RNA-Seq analysis. The original file is available from https://hpc.nih.gov/apps/singularity.html. Especially, From: is changed to use miniconda3. I have to comment out sailfish installation.

	sudo singularity build rnaseq3 rnaseq3.def
	./rnaseq3 cat /etc/os-release # debian 11, host=ubuntu 2204
	./rnaseq3 samtools --version # 1.10
	./rnaseq3 STAR --version # 2.5.2b
	./rnaseq3 fastqc -v # v0.12.1
	./rnaseq3 kallisto \| head 1 # 0.50.1
	./rnaseq3 subread # command not found
	./rnaseq3 featureCounts -v \| head # v2.0.6
	./rnaseq3 ls /opt/conda/bin
	./rnaseq3 which gcc # 10.2.1

arraytools / TCGAbiolinks-GBM.Rmd

Last active March 11, 2024 00:27

This is an updated/enhanced version of [TCGAbiolinks to DESEq2](https://rpubs.com/tiagochst/TCGAbiolinks_to_DESEq2)

	Download Raw counts
	```{r}
	library(TCGAbiolinks)

	proj <- "TCGA-GBM"
	query <- GDCquery(
	project = proj,
	data.category = "Transcriptome Profiling",
	data.type = "Gene Expression Quantification",
	workflow.type = "STAR - Counts"

arraytools / dataOutliers2.csv

Created March 8, 2024 20:46

The data is recovered from https://developer.nvidia.com/blog/dealing-with-outliers-using-three-robust-linear-regression-models/

	-3.2510638297872343	-231.0344827586207
	-2.2808510638297874	-170.68965517241372
	-2.612765957446809	-151.72413793103442
	3.1063829787234054	246.55172413793102
	3.846808510638298	246.55172413793102
	2.7234042553191484	175.86206896551727
	2.340425531914893	194.82758620689657
	2.519148936170212	158.62068965517244
	2.187234042553192	162.0689655172414
	2.187234042553192	146.55172413793105

arraytools / dataOutliers.csv

Created March 7, 2024 19:22

Test data containing outliers

	0.3114754098360656	0.4101123595505618
	0.4499089253187615	0.4082397003745317
	0.3460837887067396	0.5580524344569288
	0.8105646630236795	0.7584269662921348
	0.785063752276867	0.7584269662921348
	0.7777777777777779	0.7584269662921348
	0.7686703096539163	0.7584269662921348
	0.7231329690346083	0.7602996254681647
	0.7085610200364298	0.7602996254681647
	0.6976320582877961	0.7584269662921348

arraytools / Install_R_RStudio.txt

Last active March 26, 2025 16:51

Install multiple versions of R and launch RStudio with different versions of R. Here I assume I'm working on a Debian desktop (Linux distro affects how R is installed and the binary version of RStudio.

	# References:
	# https://cran.r-project.org/bin/linux/debian/
	# https://rviews.rstudio.com/2018/03/21/multiple-versions-of-r/
	# 2023/12/30

	sudo nano /etc/apt/sources.list # deb-src http://deb.debian.org/debian/ unstable main
	sudo apt update
	sudo apt build-dep r-base

	wget https://cran.r-project.org/src/base/R-4/R-4.3.2.tar.gz

arraytools / officer-R.Rmd

Last active December 27, 2023 22:39

A demonstration of using the 'officer' R package

	---
	title: "Officer"
	output: html_document
	date: "2023-12-26"
	---

	```{r setup, include=FALSE}
	knitr::opts_chunk$set(echo = TRUE)
	library(officer)
	library(flextable)

arraytools / Dockerfile

Last active August 5, 2024 19:42

RenvDocker example for Docker + Shiny. See https://appsilon.com/renv-with-docker/ for more details.

	# Base R Shiny image
	FROM rocker/shiny

	# Make a directory in the container
	RUN mkdir /home/shiny-app

	# Install Renv
	RUN R -e "install.packages('renv', repos = c(CRAN = 'https://cloud.r-project.org'))"

	# Copy Renv files and Shiny app

arraytools / flatpak.txt

Last active November 4, 2023 13:33

flatpak installation process

	$ flatpak install com.obsproject.Studio.flatpakref

	Note that the directories

	'/var/lib/flatpak/exports/share'
	'/home/brb/.local/share/flatpak/exports/share'

	are not in the search path set by the XDG_DATA_DIRS environment variable, so
	applications installed by Flatpak may not appear on your desktop until the
	session is restarted.

arraytools / resp.txt

Created September 28, 2023 19:29

respiratory data for running longitudinal data analysis. See the SAS document https://documentation.sas.com/doc/en/pgmsascdc/v_012/statug/statug_gee_examples01.htm.

	center id treat sex age baseline visit1 visit2 visit3 visit4
	1 1 P M 46 0 0 0 0 0
	1 2 P M 28 0 0 0 0 0
	1 3 A M 23 1 1 1 1 1
	1 4 P M 44 1 1 1 1 0
	1 5 P F 13 1 1 1 1 1
	1 6 A M 34 0 0 0 0 0
	1 7 P M 43 0 1 0 1 1
	1 8 A M 28 0 0 0 0 0
	1 9 A M 31 1 1 1 1 1