Dear developers, for your information, the Bioconductor Code of Conduct
committee's response to a violation reported at BioC2019 has been posted at
https://bioc2019.bioconductor.org/code_of_conduct.
--
Levi Waldron
Associate Professor
Department of Epidemiology and Biostatistics
CUNY Graduate
Thank you for the responses so far!
The idea behind this is that I don’t want to limit users to a certain DGE
toolkit, may it be DESeq2, edgeR or frameworks specifically developed for
single cell data such as muscat. I’d like to have a common structure that users
can pour their results into (mo
Hi Roman,
I think it is probably also helpful to check out how DESeq2 and edgeR
(two popular Bioconductor packages for differential expression analysis)
have solved that problem:
In DESeq2 for example the `nbinomWaldTest()` function calculates the
differential expression and stores the results
On Mon, Mar 9, 2020 at 6:58 AM Roman Hillje via Bioc-devel <
bioc-devel@r-project.org> wrote:
> Hi all,
>
> I was wondering if there is a class for results of differential gene
> expression analysis. I couldn’t find anything generic. Perhaps it’s too
> similar to a simple data frame, but I like th
I would imagine a SummarizedExperiment would be the best option
https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html
Lori Shepherd
Bioconductor Core Team
Roswell Park Comprehensive Cancer Center
Department of Biostatistics & Bioinformatics
Elm & Carlton Streets
Buf
Hi all,
I was wondering if there is a class for results of differential gene expression
analysis. I couldn’t find anything generic. Perhaps it’s too similar to a
simple data frame, but I like the idea of having a consistent format. I would
imagine something that holds gene names, statistics (lo
Sorry for the inconvenience. I reverted this in Biostrings 2.55.5:
https://github.com/Bioconductor/Biostrings/commit/567d8c30609783f87d7c641a98be1711ea47fb38
Using the compact ellipsis was an experiment in Bioc devel. Didn't
really like it anyway (was hard to see).
H.
On 3/9/20 01:00, Ulri
Dear colleagues,
Thanks for your replies to my message! A few more comments:
* The issue I was reporting appeared on a Linux system
(https://;www.r-project.org/nosvn/R.check/r-devel-linux-x86_64-debian-clang/apcluster-00check.html).
* I agree that this is mainly a problem related to how La
