通过conda安装纯净环境的SCENIC

发布于 2022-03-12  227 次阅读


  • https://scenic.aertslab.org/tutorials/
  • https://anaconda.org/conda-forge/r-base
  • conda create -n scenic -c conda-forge r-base=4.1.2 -y
  • conda activate scenic
  • conda install -c conda-forge r-seurat=4.1.0 -y
  • conda install -c conda-forge r-irkernel=1.3 -y
  • conda install -c conda-forge r-biocmanager=1.30.16 -y
  • conda install -c conda-forge r-devtools=2.4.3 -y
  • conda install -c conda-forge --strict-channel-priority r-arrow=7.0.0 -y
  • conda install -c bioconda bioconductor-aucell=1.16.0 -y
  • conda install -c bioconda bioconductor-rcistarget -y
  • conda install -c bioconda bioconductor-complexheatmap=2.10.0 -y
  • conda install -c bioconda bioconductor-genie3=1.16.0 -y
  • conda install -c bioconda bioconductor-biocparallel=1.28.3 -y
  • conda install -c conda-forge r-doparallel=1.0.17 -y
  • conda install -c conda-forge parallel=20220222 -y
  • conda install -c conda-forge r-foreach=1.5.2 -y
  • conda install -c maximinio r-scopeloomr=0.3.1 -y
  • conda install -c conda-forge r-rbokeh=0.5.2 -y
  • conda install -c conda-forge r-nmf=0.21.0 -y
  • wget https://github.com/aertslab/SCENIC/archive/refs/heads/master.zip -O SCENIC-master.zip
  • BiocManager::install(c("NMF", "R2HTML"))
  • BiocManager::install(c("doMC", "doRNG"))
  • devtools::install_local("SCENIC-master.zip")
  • IRkernel::installspec(name='scenic', displayname='r-scenic')
mkdir RcisTarget_data && cd RcisTarget_data
mkdir human && cd human
wget https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_r45/mc9nr/gene_based/hg19-500bp-upstream-7species.mc9nr.feather
wget https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg19/refseq_r45/mc9nr/gene_based/hg19-tss-centered-10kb-7species.mc9nr.feather

wget https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg38/refseq_r80/mc9nr/gene_based/hg38__refseq-r80__10kb_up_and_down_tss.mc9nr.feather
wget https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg38/refseq_r80/mc9nr/gene_based/hg38__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr.feather

 

总体来说,hg38相对于 hg19是一个巨大进步。by 员炊事

  1. 改变了之前的一些测序错误,组装错误。直观的例子有 degenerate bases 少了很多。
  2. 补上了hg19中的很多gap。 特别重要的是 centromere 的序列也不再是空白。hg19的时候,centromere 的部分直接就是gap, hg38后,开始有了 a-satellitle sequences。尽管只是“简单”的表现了 a-satellite repeats, 已经是一个巨大的提升。
  3. sequence 改了之后,相应的 annotation 也改了很多。比较宏观的就是 hg38 的 exome 比hg19 的大了不少。如果我的记忆没出错的话,大了25% 左右。
dbs <- list(`500bp`='hg38__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr.feather', `10kb`='hg38__refseq-r80__10kb_up_and_down_tss.mc9nr.feather')
scenicOptions <- initializeScenic(org="hgnc", dbDir="~/upload/zl_liu/RcisTarget_data/human/", nCores=10, dbs = dbs)

 

library(foreach)
library(parallel)
library(doParallel)
library(BiocParallel)

 


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