Bioconductor NcRNA

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computational biology molecular biology RNA r-loop ncRNA Job

5.1 years ago l.brown ▴ 10

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grch37 transcripts biotype biomaRt ncrna

updated 5.3 years ago by James W. MacDonald 64k • written 5.3 years ago by sergio.martinezcuesta ▴ 10

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gsea ncrna coexpression gene set analysis gene set testing

7.6 years ago m.fletcher ▴ 20

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1.0k

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biomart ncrna

updated 8.2 years ago by Thomas Maurel ▴ 800 • written 8.2 years ago by Zhang,Jiexin ▴ 20

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trna ncrna genomicfeatures featuredb biomart

updated 8.7 years ago by Hervé Pagès 16k • written 8.7 years ago by Keith Hughitt ▴ 180

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Comment: DuplicateCorrelation() block by duplicate sample or by cell line ? by Gordon Smyth 49k

They are not technical replicates. Your experiment has only one level of variability so there is no possibility of estimating random effect…

Comment: DuplicateCorrelation() block by duplicate sample or by cell line ? by Gimena • 0

Hi James, Yes, these are complete cases. every line has all the treatment groups and technical replicates.

Comment: DuplicateCorrelation() block by duplicate sample or by cell line ? by Gimena • 0

I am sorry for the confusion. It goes like this: 3 drug exposures (vehicle, low and high dose) x 2 replicates per condition: technical re…

Comment: How does Deseq2 deal with the row with zero when calculating size factors by jiakang • 0

Thanks for your quick reply. I understand and have noticed the code you mentioned above. > the size factors results of sfType = "poscount…

Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0

Yes. I considered genome wide p value as cutoff.

Votes

Attempting to import SBML file using R

Answer: RNASeq time course analysis, missing time points for control

Answer: biomaRt not working - lazy table error

Answer: Confused about the CPM and TMM normalization in edgeR

Answer: Differential gene expression analysis

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