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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 |
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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" |
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-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 |
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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 |
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# 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 |
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--- | |
title: "Officer" | |
output: html_document | |
date: "2023-12-26" | |
--- | |
```{r setup, include=FALSE} | |
knitr::opts_chunk$set(echo = TRUE) | |
library(officer) | |
library(flextable) |
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# Base R Shiny image | |
FROM rocker/shiny | |
# Make a directory in the container | |
RUN mkdir /home/shiny-app | |
# Install Renv | |
RUN R -e "install.packages('renv', repos = c(CRAN = 'https://cloud.r-project.org'))" | |
# Copy Renv files and Shiny app |
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$ 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. |
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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 |
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