create_cisTarget_databases

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Recently, I created goat feather files but I didn't know how to use the feather file as the R SCENIC input file here is my code  ``` library(Seurat) library(tidyverse)...

CNChunhua

Can I use this method to create a cisTarget database for plant?

1

Hi , I collated the motif information of Arabidopsis thaliana from JASPER database,and I have successfully run the script . I wonder if this method is suitable for the creation...

cheer1104

How to deal with genes or regions in human unmapped in other species by liftover

1

Hi, I have a problem when using create_cross_species_motifs_rankings_db.py to get the ranking file. Before this step: (1). ~20,000 human genes were selected, which in the hg19-500bp-upstream-7species.mc9nr.genes_vs_motifs.rankings.feather. (2). I downloaded fasta...

yangliu0729

Can I apply cisTarget to estimate the RBP-regulon?

6

Hi, I have binding sites of RNA binding proteins (RBP) analyzed from CLIP-seq data, so I want to do the motif enrichment and RBP-regulon prediction, which's used as input for...

kerenzhou062

Build the Axolotl cisTarget database issue

14

Hi,@authors： I built the Axolotl cisTarget database just following the instruction of Gallus gallus cisTarget [database.](https://github.com/aertslab/create_cisTarget_databases/issues/4) First， I got the Axolotl gene 10kb up- and 10kb downstream of the TSS...

fengweimin-maker

create_cistarget_motif_databases issues

2

Thanks for your detailed explanation! It is very helpful. Could you also pls guid me if I want to create a track-based database? I have the region fasta file and...

huoqiang138

Good afternoon- Can you please add a license to this repo? Thanks

asistradition

create the mouse database with an additional motif

6

Hi @tropfenameimer, I need to create the mouse database with an additional motif. In order to run create_cisTarget_databases the procedure say that you need the motif collection and the FASTA...

tropfenameimer

The public motif collection PWMs for motifs-v9-nr

1

Thanks for providing the SCENIC+ public motif collection PWMs , it is very helpful ! I noticed that the version of the motif collection is "V10: 2022 SCENIC+ clustered motif...

QianzhaoJ

Try to create the chicken cisdatabase

8

Hello,I'm trying to create the chicken's cistarget database for my single-cell research analysis, and already creating the GRCg6a.regions_vs_motifs.rankings.feather throught EPD's bed and v10_clust motifs. But when i try to run...

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