mc9nr (DEPRECATED): cisTarget databases generated using the 2017 cisTarget motif collection. mc_v10_clust (RECOMMENDED): cisTarget databases generated using the 2022 SCENIC+ motif collection. tc_v1: cisTarget databases generated using ENCODE ChIP-seq tracks (2,993 tracks). 目前软件作者推荐的是...
scenicOptions <- initializeScenic(org = "mgi", dbDir = "cisTarget_databases", nCores = 1) # scenicOptions@inputDatasetInfo$cellInfo <- 'int/cellInfo.Rds' saveRDS(scenicOptions, file = "int/scenicOptions.Rds") 2.构建基因共表达网络 ### Co-expression network genesKept <- geneFiltering(expr...
cd data 进入文件夹 先运行如下命令下载一个文件 用来检查数据完整性。 # Download sha256sum.txt (with wget or curl):wget https://resources.aertslab.org/cistarget/databases/sha256sum.txt 得到sha256sum.txt 内容如下: image.png 然后把你下载的文件逐个放进data文件去检查。 运行如下一句命令 awk -v...
dbFiles <- c("https://resources.aertslab.org/cistarget/databases/mus_musculus/mm9/refseq_r45/mc9nr/gene_based/mm9-500bp-upstream-7species.mc9nr.feather", "https://resources.aertslab.org/cistarget/databases/mus_musculus/mm9/refseq_r45/mc9nr/gene_based/mm9-tss-centered-10kb-7species.mc9nr....
mc_v10_clust (RECOMMENDED): cisTarget databases generated using the 2022 SCENIC+ motif collection. tc_v1: cisTarget databases generated using ENCODE ChIP-seq tracks (2,993 tracks). 目前软件作者推荐的是 新版:https://resources./cistarget/databases/homo_sapiens/hg38/refseq_r80/mc_v10_clust/gen...
library(RcisTarget) library(loomR) 3.2.2 下载数据库 比如说创建一个cisTarget_databases目录,然后根据对应物种下载相应的数据库文件到目录下。下面示例为用R下载,也可以wget等其他方法。 准备工作:下载评分数据库 dbFiles <- c('https://resources.aertslab.org/cistarget/databases/mus_musculus/mm9/refseq_r45...
# 保证cisTarget_databases 文件夹下面有下载好2个1G的文件 scenicOptions <- initializeScenic(org="hgnc", dbDir=db , nCores=4) saveRDS(scenicOptions, file="int/scenicOptions.Rds") saveRDS(cellInfo, file="int/cellInfo.Rds") ### Co-expression network genesKept <- geneFiltering(exprMat, scenic...
scenicOptions <- initializeScenic(org = "mgi", dbDir = "cisTarget_databases", nCores = 1) # scenicOptions@inputDatasetInfo$cellInfo <- 'int/cellInfo.Rds' saveRDS(scenicOptions, file = "int/scenicOptions.Rds") 2.构建基因共表达网络
scenicOptions <- initializeScenic(org="mgi", dbDir="cisTarget_databases", nCores=10) Note that I had to use old versions of the mouse database feather files available here: https://resources.aertslab.org/cistarget/databases/old/ running initializeScenic generates the error message: Motif data...
The new databases can be downloaded fromhttps://resources.aertslab.org/cistarget/. 2018/03/30: New releases pySCENIC: lightning-fast python implementation of the SCENIC pipeline. Arboretopackage includingGRNBoost2and scalableGENIE3: Easy to install Python library that supports distributed computing. ...