Bioconductor Submit package

Showing : submit package • reset

votes

862

views

bioconductor submit package

updated 7.0 years ago by Martin Morgan 25k • written 7.0 years ago by Jurat Shahidin ▴ 80

vote

replies

954

views

package submit package package updates

7.3 years ago francescodc87 • 0

votes

replies

968

views

news package submit package News

updated 7.3 years ago by Martin Morgan 25k • written 7.3 years ago by Valerie Obenchain ★ 6.8k

votes

replies

1.4k

views

submit package tracker build report

7.4 years ago thomas.nigel.lawson • 0

vote

replies

1.0k

views

submit package experimentdata

updated 7.6 years ago by Martin Morgan 25k • written 7.6 years ago by mark.dunning • 0

vote

replies

1.4k

views

submit package

updated 8.3 years ago by James W. MacDonald 63k • written 8.3 years ago by hong.wang • 0

6 results • Page 1 of 1

Recent ...

Replies

Comment: DESeq2, results(dds, name = <reference>) interpretation results by Rockbar • 0

When I apply the model.matrix approach for getting the contrasts, the code > mod_mat <- model.matrix(design(dds), colData(dds)) > CondA.t…

Comment: DESeq2, results(dds, name = <reference>) interpretation results by Rockbar • 0

Yes, I agree, the correct contrast setting is quite challenging. The vignette says >contrast: a list of 2 character vectors: the names of…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

Advantage and disadvantage depends on the aim, what you plan to do with them (testing, plots, etc.). lengthScaledTPM puts back *in* the ge…

Comment: DESeq2, results(dds, name = <reference>) interpretation results by James W. MacDonald 63k

No, putting -1 in the design matrix is a cell means model, which is the opposite. If you used `~ Cond + Cond:Time`, you would specify a fac…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0

Thank you for the response and apologies for my late reply. I think I´m starting getting the concept now. The hints with the cqn is quite …

Votes

Answer: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?

Answer: Remove duplicates of colData in TreeSummarizedExperiment

Awards • All

Scholar to James W. MacDonald 63k