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genomicfeatures genomicranges cds overlap

updated 9.0 years ago by Michael Lawrence ★ 11k • written 9.0 years ago by madsheilskov ▴ 10

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txdb granges cds orf R

updated 6.5 years ago by James W. MacDonald 67k • written 6.5 years ago by q.thomas • 0

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cds

9.0 years ago KB ▴ 50

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Annotatr CDS Exon UTR

updated 6.8 years ago by rcavalca ▴ 140 • written 6.8 years ago by xie186 • 0

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genomicfeatures txdb.hsapiens.ucsc.hg19.knowngene cds

8.2 years ago madsheilskov ▴ 10

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biomart bioconductor grangeslist cds ribosome profiling

updated 7.5 years ago by Hervé Pagès 16k • written 7.5 years ago by Walter F. Baumann ▴ 10

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genomicfeatures genomicranges cds overlap

updated 3.0 years ago by balajee • 0 • written 9.0 years ago by madsheilskov ▴ 10

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genomeintervals UTRs exons CDS GenomicRanges

updated 7.3 years ago by Michael Lawrence ★ 11k • written 7.3 years ago by rubi ▴ 110

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Comment: Differential Expression Genes as Independent Variables by Dario Strbenac ★ 1.5k

Also, the reason why gene abundance is the dependent variable and is iterated over is that there are far more genes than there are samples …

Comment: rrvgo::calculateSimMatrix() error by Phila • 0

Thanks for sharing the solution. It helps me. [nced cloud][1] [1]: https://my-ncedcloud-login.us/

Comment: Merge Replicates vs Mixed Model by gabriel.hoffman ▴ 170

For your proteomics data, your normalization is correct. I had assumed it was RNA-seq because that is what I think about most. When using…

Comment: What type of counts data to import for performing Isoform analysis in edgeR by mohammedtoufiq91 ▴ 10

@gordonsmyth I will re-run Salmon with the --numGibbsSamples=50 option. Thank you.

Comment: Differential Expression Genes as Independent Variables by Gordon Smyth 52k

Such an analysis cannot be done in limma. Sorry, I cannot tell you how to do it or even whether it is possible.

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Comment: What type of counts data to import for performing Isoform analysis in edgeR

Answer: What type of counts data to import for performing Isoform analysis in edgeR

Transcript-level differential expression using DESeq2

Comment: What type of counts data to import for performing Isoform analysis in edgeR

Answer: What type of counts data to import for performing Isoform analysis in edgeR

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