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Hi,
This is not a technical issue but a conceptual question.
Till date, I have been using HOMER for ChIP-seq and ATAC-seq peak annotation. As I intend to perform TOBIAS DNA foot printing analys…
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options("repos"= c(CRAN="https://mirrors.tuna.tsinghua.edu.cn/CRAN/"))
options(BioC_mirror="http://mirrors.tuna.tsinghua.edu.cn/bioconductor/")
BiocManager::install("ChAMP")
BiocManager::install("C…
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Hello,
Thank you for the great tool.
One question I have after reading the paper, also looking the code, is seems that the peak-gene pairs are predicted using cells from one cell type (cluster)…
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**Reported by cmungall on 2008-11-12 13:01 UTC**
The following triads show terms with >1 asserted is_a parent. Ideally each term should have 1 asserted is_a parent/genus. If there are more then the…
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**Reported by cmungall on 2008-01-29 00:45 UTC**
in general a class should have zero, two or more subtypes.
eg
single_is_a_child SO:0000872-trans_spliced_mRNA SO:0000479-trans_spliced_transcript
…
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Brought to my attention by Colin Logie
**What is the SO term name and accession?**
intronic_splicing_silencer (SO:0002056)
exonic_splicing_silencer (SO:002058)
Both are children of silencer (SO:…
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I think it would be a useful exercise to find a paper or two which use one of the existing tools (UCSC, Wash U epigenome browser) to test hypotheses related to gene regulation (ideally using some Cist…
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Hollis (@wrighth) is working on 3d visualization tooling for networks.
He is looking for potential datasets so Shannon McWeeney sent him our way.
Attached is an example of the format would needs the…
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@rawnakhoque I asked the PDF in our lab and he showed me that everything has been done in bash. Follow the installation and basic configuration step by step [here](http://homer.ucsd.edu/homer/introduc…
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Hello, I'm trying to replicate your prediction results for "CD4-positive_helper_T_cell-ENCODE" published in [Nature at 2021](https://www.nature.com/articles/s41586-021-03446-x#Sec9): as shown in the […