Showing : deconstructsigs • reset
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tri.counts.method parameter in deconstructSigs
deconstructsigs
updated 5.9 years ago by 0 • written 7.8 years ago by ▴ 90
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Is there any way to write my mutation dataframe to vcf file?
writevcf vcfr mutationalpattern deconstructSigs synbreed
updated 6.5 years ago by 4.1k • written 6.5 years ago by ▴ 50
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Comment: ANOVA like approach of edgeR by Yunshun Chen ▴ 870
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 ▴ 870
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…
Comment: CleanUpRNAseq with a GTF that is missing mitochondria annotation data by rcreed • 0
The updated version worked well on my data. Thank you!
Votes
A: ANOVA-like test with edgeR
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data
A: TopGO: How to retrieve the gene list related to a GO ID ?
A: Error in DESeqDataSet : some values in assay are not integers
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