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How can I translate NM_xxx.y:c.xxG>C mRNA sequences to corresponding NC_xxx.y:g.xxxC>G chromosomal coordinates?
refseq Bioconductor conversion
9 months ago heiko_kin ▴ 50
1
vote
7
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364
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BioMart webservices broken?
software error ensemblID conversion
updated 2.2 years ago by 58k • written 2.2 years ago by • 0
2
votes
1
reply
624
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Convert Flowframe to matrix
flowcore fcs flow cytommetry matrix conversion
updated 2.3 years ago by ▴ 280 • written 2.3 years ago by • 0
3
votes
6
replies
775
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biomaRt: Ensembl -> Entrez conversion error?
biomart entrez gene identifiers ensembl conversion
updated 2.8 years ago by ★ 5.1k • written 2.8 years ago by ▴ 10
3
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3
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1.0k
views
Does AnnotationHub replaces AnnotationDbi for ID conversion (e.g. entrez, refseq, symbols)?
conversion symbol entrez
updated 6.0 years ago by 58k • written 6.0 years ago by ▴ 40
5 results • Page 1 of 1
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Answer: Error in makeTxDbFromGFF(txomeInfo$gtf) by Michael Love 34k
I see that tximeta found a linked transcriptome. Can you show this part of your code as well? How did you create the `linkedTxome`?
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Gordon Smyth 43k
You need to start by doing an ordinary paired analysis.
Comment: Recalculated abundance data output table with DEseq2 by Michael Love 34k
Yes, DESeq() then results(). When you print the table it will say MLE. No we don’t have a function to do that.
Comment: Recalculated abundance data output table with DEseq2 by michael.morash • 0
Thanks for getting back to me so quickly. The final comparison we are looking to report are the effects of filtering out low count genes us…
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Field -Ye • 0
Hi Professor Smyth, Thank you for pointing me to your previous publication. I went through the verbal part and found you did pursue the DG…
Votes
Answer: Degust: what normalization method does it use
Answer: ylim and xlim in Enhanced Volcano
Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi
Error in .rowNamesDF<-(x, value = value) :duplicate row.names are not allowed DESeq2
Comment: How to build a GRangesList where each GRanges element is a CDS coordinate of gen
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