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I have four different 10x multiome seurat object (one for each experiment). I am able to integrate the RNA assay without much issue.
```r
merge_obj
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Hi,
I have some some bulk ATAC and RNA seq in which I wanted to identify some DORCs. Is it possible to use the dorc function in this kind os data (ie importing my bulk rds into the objects)? Of cour…
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- https://github.com/ENCODE-DCC/rna-seq-pipeline
- https://www.genome.gov/sites/default/files/Multimedia/Slides/ENCODE2016-ResearchAppsUsers/ENCODE2016_strattan_slides.pdf
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Hello,
I noticed there was code for evaluation in issue 29, but I want to ask the specific code used for calculating the insulation score, ''import insulation as insu''.
Additionally, I am intri…
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Hi @davek44
we have ATAC-seq data in different tissues and we want use the basenji to predict the activaty of snps. We wonder we put all the ATAC-seq in different tissues togother to the bsenji for…
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Hi there, thanks for this helpful package!
I am integrating single-cell RNA-seq and ATAC-seq data where one cluster is missing in one dataset, so the sizes of the two datasets are different. I can…
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> @mtxellrb A script for creating a track database from bigWig TF ChIP-seq data is now added :`create_cistarget_track_databases.py`
>
> https://github.com/aertslab/create_cisTarget_da…
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I was wondering why the ChIP-Seq pipeline doesn't include an adapter trimming step like in the ATAC-Seq pipeline. Are adapter-trimmed FASTQs required for this pipeline?
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## **Describe the bug**
Hi team,
I tried to peak-call using input files as dedupped BAM files. It worked initially for 1 sample (2 replicates), but not for the second sample.
## **OS/Platform**…
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I tried the example json on the SCG cluster, and it exited with errors. I read in another issue that this type of error can occur if installed with mamba. However, I did not install with mamba. Please…