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Dear processors,
Thank you for developing this tool. I used it to generate results and found that some of the enriched genes are located in repetitive sequences. Should I simply ignore these genes,…
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Real data sources to use:
1. Mutations from the [AWS S3 MultiAssayExperiment for ACC](https://github.com/waldronlab/MultiAssayExperiment/blob/master/inst/extdata/miniACC.R)
2. ABSOLUTE copy number c…
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Hello. I believe ChromDiff is still recommended for finding out regions with differential chromatin state and linking it with different expression.
I'd like to give it a try, but I have not been able…
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Hi,
I hope all is well. I have cell-specific open chromatin regions that I'm trying to run S-LDSC with. The problem is that the annotations resulting from these files are very small and don't cover…
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FYPO uses some EQs using [RO:0001025](https://www.ebi.ac.uk/ols/ontologies/ro/properties?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FRO_0001025), located in, in conjunction with SO terms such as
…
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Hi,
I was wondering if adding the feature of shifting and splitting the reads after the alignment would be helpful.
A recent review on the approaches to analyze ATAC-seq data ([Yan et al., 2020]…
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Since SNPs that are close to each other are passed down together in populations, genetic variability can separate different countries and geographical locations to a certain extent (see links). It wou…
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**Project:**
Pseudo-WGS variant calling for common cell lines mining ENCODE and Roadmap Epigenomics data Recent progress in sequencing technologies have led to a massive production of epigenetic datas…
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**What is this request referring to?**
Defining regions of nucleosome occupancy
**What is the name you would like SO to give the term?**
Nucleosome_occupancy
**What is the definition that you …