20221011-R和R包安装 Rnaseq

quantification

source("http://bioconductor.org/biocLite.R")
biocLite("Rsubread") limma edgeR
library("Rsubread") limma edgeR失败
conda install bioconductor-edger
conda install bioconductor-limma
conda install biocnoductor-rsubread
conda install -c bioconda bioconductor-deseq2
conda install -c bioconda bioconductor-rsubread
conda install -c bioconda bioconductor-edger



Rscript run-featurecounts.R -b ../1.mapping/BLO_S1_Rep1.bam -g ../refgenome/gene.gtf -o BLO_S1_Rep1
conda install biocnoductor-argparser
install.packages("argparser")
conda install biocnoductor-rsubread
install.packages("BiocManager")
BiocManager::install("Rsubread")
BiocManager::install("edgeR")
install.packages("edgeR")

source("http://bioconductor.org/biocLite.R")
#指定一个离你最近的国内镜像
options(BioC_mirror="http://mirrors.ustc.edu.cn/bioc/")
biocLite("edgeR")

install.packages('edgeR',repos='http://cloud.r-project.org')
conda install -c bioconda bioconductor-rsubresad




Bioconductor version 3.8 (BiocManager 1.30.18), R 3.5.0 (2018-04-23)
library("rsubread")
BiocManager::install("Rsubread")
BiocManager::install("degeR")


Description:    Ubuntu 18.04.4 LTS
sudo su
echo "deb http://www.stats.bris.ac.uk/R/bin/linux/ubuntu bionic-cran40/" >> /etc/apt/sources.list
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
apt-get update
apt-get upgrade

###重装系统
wget https://repo.anaconda.com/archive/Anaconda3-2020.11-Linux-x86_64.sh
bash *.sh
sudo vi /etc/profile
export PATH=$PATH:/home/messia/anaconda3/bin
source /etc/profile
source .bashrc

conda create -n r3.6
conda activate r3.6
conda install r-base=3.6
conda deactivate

R version 3.6.1 (2019-07-05)

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install(version = "3.10")

library("BiocManager")
Bioconductor version 3.10 (BiocManager 1.30.18), R 3.6.1 (2019-07-05)
Bioconductor version '3.10' is out-of-date; the current release version '3.15'
  is available with R version '4.2'; see https://bioconductor.org/install

BiocManager::install("ggplot2")
BiocManager::install("Rsubread")
BiocManager::install("edgeR")
***
Warning: dependency ‘locfit’ is not available
***
BiocManager::install("locfit")
install.packages('https://cran.r-project.org/src/contrib/Archive/locfit/locfit_1.5-9.2.tar.gz',repos = NULL)

BiocManager::install("limma")


library("ggplot2")
library("Rsubread")
library("degeR")
library("limma")

conda 更新
conda install fastp
conda install hisat2
conda install samtools

ascp密钥
/home/ubuntu/anaconda3/etc

Rscript run-featurecounts.R -b ../2mapping/BLO_S1_Rep1.bam -g ../refgenome/gene.gtf -o BLO_S1_Rep1