Decontam与SCRUB：安装与使用

Decontam安装

GitHub - benjjneb/decontam: Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

准备Rstudio

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

BiocManager::install("decontam")

library(devtools)
devtools::install_github("benjjneb/decontam")
install.packages("phyloseq")
library("decontam")

Introduction to decontam

https://benjjneb.github.io/DecontamManuscript/Analyses/oral_contamination.html

具体使用见这两个官方文档

SCRUB安装

install.packages( c('glmnet', 'torch', 'tidyverse') )
devtools::install_github("shenhav-and-korem-labs/SCRuB")
library(SCRuB)

GitHub - Shenhav-and-Korem-labs/SCRuB

具体使用方法见上述官方文档