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When generating a matrix of features for RIVER, how do the developers handle situations where no variant near a particular gene has a CADD annotation for features like TFBS or EncOCCombPVal? glmnet ca…
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Hello,
I used chromstaR package in our lab. It was easy to use but I need a bit of your help to understand the computational aspect of it. I sincerely thank you for your time.
 from your paper (**Decoding the spatial chromatin organization …
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Dear
I am trying to do allelic analysis Hic data getting same error G2 is mapping reads are zero and iced normalisation step getting error. I used bellow command to run analysis. non allelic analysi…
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### Data Owner Name
ENCODE Data Coordinating Center
### Data Owner Country/Region
United States
### Data Owner Industry
Life Science / Healthcare
### Website
https://www.encodeproject.org/
###…
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Hi!
Have you explored strategies for batch integration for larger datasets or sample normalisation in addition of the scaling/log normalisation?
Any advice?
Thanks!
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Hi Dr. Shao,
I'm generating the TT-seq analysis to see the influence of acute degradation of a TF on the transcription of mRNAs and eRNAs. I find your transcription unit annotation script - TU_filt…
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Hello!
CellxGene is by far my favourite viewer and kudos for doing a great job developing it and maintaining it!
What are the odds of extending cellxgene to handle other data modalities? I am no…
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I read quite a few papers today that refer to "Transcriptional gene silencing (TGS)
This used to be an independent term, but it is now a synonym of heterochromatin assembly, but it seems narrower.…
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@matentzn I am attempting to run the release pipeline after adding new phenotype classes based on the most recent XAO additions. I am getting errors for "849 unsatisfiable classes in the ontology" fro…
seger updated
3 weeks ago