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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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hg19-500bp-upstream-7species.mc9nr.feather file is not available for download #332

Closed ZainulArifin1 closed 1 year ago

ZainulArifin1 commented 1 year ago

Hi!

I tried performing a tutorial of scenic with R on this page. But I had trouble with initializing scenic with "initializeScenic" function because hg19-500bp-upstream-7species.mc9nr.feather is not available in https://resources.aertslab.org/.

Is there an equivalent of this file or is there a link to a repo where I can download this file from? Thank you.

tfguinan commented 1 year ago

Hi there, I'm in the same boat as you, unable to follow the setup vignette due to 404 error.

After having a look through the index of https://resources.aertslab.org/ I came across an 'old' directory with similar data: https://resources.aertslab.org/cistarget/databases/old/homo_sapiens/hg19/refseq_r45/mc9nr/gene_based/

From the naming conventions the hg19-500bp-upstream-7species and hg19-tss-centered-5kb-7species .mc9nr.feather should be somewhat equivalent to those outlined albeit with a lower kb/TSS region. Perhaps I'm mistaken but I suspect the 5kb data reflects that of the 2017 publication (5kb up/down for 10kb around the TSS).

The .mc9nr.feather(s) are downloading, and I'll test them in SCENIC referring to the introduction vignette. Maybe a member of the team could clarify distinctions of these various databases for us.

Cheers.

tfguinan commented 1 year ago

Hi just following up - I was able to successfully run 'initializeScenic' using the aforementioned datasets. 'scenicOptions' was also valid input for a number of the downstream functions.