Showing : makeTxDbFromGRanges • reset
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troubleshooting makeTxDbFromGRanges: some exons are linked to transcripts not found in the file
genomicfeatures txdb makeTxDbFromGRanges
updated 9.5 years ago by 16k • written 9.5 years ago by ★ 4.1k
2
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make TxDb from list of genes
R maketxdbfrombiomart maketxdbfromgranges rstudio ensembl
updated 2.7 years ago by ▴ 10 • written 7.1 years ago by • 0
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error with makeTxDbFromGFF
genomicfeatures gff custom genome makeTxDbFromGFF makeTxDbFromGRanges
6.8 years ago xvazquezc • 0
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1.8k
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error when creating txdb from gtf
genomicfeatures makeTxDbFromGRanges GenomicFeatures makeTxDbfromGRanges
updated 5.5 years ago by 4.3k • written 5.5 years ago by • 0
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Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
limpa reads standard feature-level output from Spectronaut. You do not need to make any changes to the output before reading it into limpa.…
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Comment: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by JKim • 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
Yes, making a group factor simplifies things, and you will need a new column for disease subject to avoid having a design that is not full …
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Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
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