pliu55 comments

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                                            pliu55

MPAC

Thanks for all the suggestions, @vjcitn. I will utilize SummarizedExperiment as you recommended. For PARADIGM, I will remove the github URLs from the code. This will likely lead to reduced...

Hi @vjcitn and @lshep, Thanks again for your suggestions. I have improved the [MPAC package](https://github.com/pliu55/MPAC) accordingly. All the changes are listed in the [NEWs.md](https://github.com/pliu55/MPAC/blob/main/NEWS.md). Specifically, - Use of SummarizedExperiment objects...

MPAC

Hi @lshep and @vjcitn, According to the [build report](http://bioconductor.org/spb_reports/MPAC_buildreport_20240404181910.html) above, my package has pass all the tests except the error below: > ERROR: Subscribe to the Bioc-devel mailing list by...

MPAC

Hi @lshep, Thanks for your response. I did receive a confirmation email. I clicked the confirmation link and received a 'Welcome' email as below. In addition, I can visit [the...

Cannot run IDR with more than 2 replicates

According to Section '4d. Select final peak calls - conservative set' in [ENCODE3 ChIP-seq pipeline specifications](https://docs.google.com/document/d/1lG_Rd7fnYgRpSIqrIfuVlAz2dW1VaSQThzk836Db99c/edit#): > If you have more than 2 true replicates select the longest peak list...