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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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read in the mm10 specific feather files #208

Closed sylestiel closed 2 years ago

sylestiel commented 3 years ago

@s-aibar

Can anyone assist me with the scripts needed to read in the mm10 specific feather files? Something is amiss. Despite downloading the mm10 specific files to the dbDir cisTarget_databases the error reads as follows:

Error in initializeScenic(org = "mgi", dbDir = "cisTarget_databases", : The following RcisTarget databases were not found: - cisTarget_databases/mm9-500bp-upstream-7species.mc9nr.feather - cisTarget_databases/mm9-tss-centered-10kb-7species.mc9nr.feather Make sure the arguments 'dbDir' and 'dbs' are correct.

Originally posted by @sylestiel in https://github.com/aertslab/SCENIC/issues/18#issuecomment-867945269

cytokine4242 commented 2 years ago

Changing the DefaultDbNames to the mm10 files worked for me.

defaultDbNames$mgi[1] <- "mm10__refseq-r80__10kb_up_and_down_tss.mc9nr.feather"
defaultDbNames$mgi[2] <- "mm10__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr.feather"
defaultDbNames
scenicOptions <- initializeScenic(org="mgi", dbs = defaultDbNames[["mgi"]], dbDir="cisTarget_databases", nCores=4)
sylestiel commented 2 years ago

Hi cytokine4242,

I will definitely give it a try.

Thanks! sylestiel

On July 12, 2021 at 8:51 PM cytokine4242 @.***> wrote:

Changing the DefaultDbNames to the mm10 files worked for me.

defaultDbNames$mgi[1] <- "mm10__refseq-r80__10kb_up_and_down_tss.mc9nr.feather"
defaultDbNames$mgi[2] <- "mm10__refseq-r80__500bp_up_and_100bp_down_tss.mc9nr.feather"
defaultDbNames
scenicOptions <- initializeScenic(org="mgi", dbs = defaultDbNames[["mgi"]], dbDir="cisTarget_databases", nCores=4)

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