create_cisTarget_databases

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The 'zsync' files of databases file might be incorrect.

5

I'm sorry for submitting an issue here. I tried to download these databases using zsync. https://resources.aertslab.org/cistarget/databases/homo_sapiens/hg38/screen/mc_v10_clust/region_based/hg38_screen_v10_clust.regions_vs_motifs.scores.feather Pay attention to the SHA-1 checksum. ```bash $ sha1sum hg38_screen_v10_clust.regions_vs_motifs.scores.feather 57b58cbc57002e2b96f4b51d6a9fec0e831abd29 hg38_screen_v10_clust.regions_vs_motifs.scores.feather $ wget...

NirvanaCh7

PWMs in motif collection.

1

Hello! I was wondering whether PWM is used interchangebly with PFM in the motif collections? It says "The files named metacluster_*.cb contain position weight matrices (PWMs) for multiple motifs." in...

FelixWaern

how to get the 'genes_vs_motifs.rankings.feather'

3

Hi, firstly, i want to verify whether the output ''genes_vs_motifs.rankings.feather' and ''motifs_vs_genes.rankings.feather' is the same result. Secondly,  i followed the steps above and generated the results but without the...

krayon4river

Problems encountered during the construction of the Red Eared Turtle database

4

Dear author,  I built the library based on the method mentioned in the library building example you provided. In the end, your code will generate 8 feature files, but...

zhongguodiyidao

Creating a cisTarget database for Plant

1

I don't know how to create a cisTarget database for strawberry. I am looking forward a protocol in detail.

wujiayi666-star

build the Gallus gallus cisTarget database issue

10

Hi @ALL, i wish to build the Gallus gallus on my own, but i can really understand the input file, like below picture:  where was the Gallus gallus motif...

honghh2018

build mm10 regions based databases

4

First thank for sharing such a powerful pipeline for chromatin and motif analysis. I was trying build a mm10 database based on regions defined in ATACseq following your tutorial. However,...

WGLUN

FASTA Input to Generate SCENIC+ Databases for Rat

2

Hello, Thanks for the helpful tutorial. I am trying to generate the relevant database files to use SCENIC+ for rat genome. I've generated the motifs table by using the motifs-v10-nr.mgi-m0.00001-o0.0.tbl...

jonhsussman

convert SCENIC+ public motif collection to HOMER format

1

Hello, Can the database be converted to HOMER format with Log odds detection threshold? Thank you.

pchiang5

How to check which genes are in the database?

4

Hi, I'm using pySCENIC to analyze human iPSC data. We are interested in some genes and have the following questions: 1. We cannot find TBXT in the pySCENIC. Instead, we...

linxy29