Feng Yan

About FIMO finding putative TFBS in the tutorial.

3

I read the CENTIPEDE manuscript. I think the author scanned all putative TFBS across the genome. However, in your tutorial, you suggested using FIMO only to obtain TFBS in peak...

Feature requeste for full join of GRanges

11

Hi All, I've been working on combing GRanges from several datasets, and wish to have a function from your package that works similar to the tidyverse `full_join` which includes any...

Is it possible to change color of nodes for cnetplot.compareClusterResult

1

Hi Dr Yu, Is it possible to change color of nodes for cnetplot.compareClusterResult and emapplot.compareClusterResult? By default the nodes are colored based on clusters, using ggplot color scheme. For example:...

Hi team, Could you provide the conda version of your latest python3 rgt toolkits (0.13.1)? Cheers,

Hi team, I'm following your document from https://huishenlab.github.io/biscuit/ to analyse RRBS data. The command I'm using is ``` biscuit align -t 12 -M -R "@RG\tID:1\tSM:'$BASE'" $REF $FILE | \ samblaster...

Hi, I'm currently using your package to visualize the RRBS data, following an example from [here](https://zvfak.blogspot.com/2015/03/using-genomation-to-analyze-methylation.html). Although some of the original links doesn't work now. I managed to manual download...

Not working for UCSC fasta and annotation

1

Hi team, thanks for developing this wonderful tool. I just want to confirm if it is designed not to support UCSC genome and annotation files? I found if I use...

questions about how to get genes from the output

4

# Please report - [x] version of RNA-Bloom with `java -jar RNA-Bloom.jar -version` RNA-Bloom v2.0.1 - [x] version of java with `java -version` openjdk version "18.0.1" 2022-04-19 - [x] exact...

empty output file

4

Hi team, I tried BS-Snper on my RRBS data. The methylation calling and intermediate files were generated, but the final output is empty, however. I followed exactly your example code,...

two fastq files were not correctly formated

3

Hi team, I have downloaded some cDNA fastq files from you s3 repo. I found 2 files are not correctly formatted when I run QC with NanoPlot. ``` SGNex_MCF7_cDNAStranded_replicate2_run1/SGNex_MCF7_cDNAStranded_replicate2_run1.fastq.gz SGNex_K562_cDNAStranded_replicate3_run3/SGNex_K562_cDNAStranded_replicate3_run3.fastq.gz...