Bioconductor BiocWorkflowTools

Showing : BiocWorkflowTools • reset

votes

1.2k

views

BiocWorkflowTools

3.9 years ago c.poulton • 0

votes

replies

742

views

BiocWorkflowTools rmarkdown

4.5 years ago helucro ▴ 70

votes

replies

1.2k

views

BiocWorkflowTools

updated 4.7 years ago by Mike Smith ★ 6.6k • written 4.7 years ago by alan.ocallaghan ▴ 160

vote

replies

1.7k

views

workflows biocworkflowtools bioconductor

6.5 years ago Koki ▴ 10

votes

800

views

biocworkflowtools

updated 6.6 years ago by Mike Smith ★ 6.6k • written 6.6 years ago by shbrief ▴ 20

votes

replies

1.9k

views

BiocWorkflowTools rmarkdown

updated 7.4 years ago by Andrzej Oleś ▴ 750 • written 7.4 years ago by Leonardo Collado Torres ★ 1.1k

6 results • Page 1 of 1

Recent ...

Replies

Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k

I'm adding my comment to the threaded section ... I don't have any suggestions here but whatever method you're using is not appropriate up…

Comment: ANOVA like approach of edgeR by Yunshun Chen ▴ 880

If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …

Comment: ANOVA like approach of edgeR by SamGG ▴ 350

Simply remove the cell type from the model. design <- model.matrix(~targets$Status)

Answer: ANOVA like approach of edgeR by Yunshun Chen ▴ 880

You could try the followings: > design <- model.matrix(~ 0 + group) > contrast <- makeContrasts(PvsL = 0.5*(L.pregnant + B.pregnan…

Answer: Identical samples after deseq2 batch effect removal by maripane • 0

Thanks Michael, so is there a way to work around this issue? Can I somehow make sure I can remove this batch effects without overcorrecti…

Votes

Answer: ANOVA like approach of edgeR

A: ANOVA-like test with edgeR

Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data

A: TopGO: How to retrieve the gene list related to a GO ID ?

Awards • All