Showing : ribosome profiling • reset
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Can I use translation efficiency counts (Ribosome profiling TPM/RNASeq TPM) as an input for DESq2 in order to perform Differential Translation analys…
deseq2 differential translation ribosome profiling
updated 22 months ago by 34k • written 22 months ago by • 0
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How to align to genome and transcriptome coordinates at the same time with STAR?
aligning ribosome profiling RNA-Seq
2.0 years ago Crispy • 0
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4
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446
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DESeq2 Ribosome Profiling Time-series: Significantly Different Results for Wald and LRT test
deseq2 ribosome profiling wald lrt
updated 2.7 years ago by 34k • written 2.7 years ago by ▴ 20
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Ribo-seq/RNA-seq analysis -- DESeq2 multi-factor design
deseq2 sequencing ribosome profiling riboseq multiple factor design
updated 3.1 years ago by 34k • written 3.1 years ago by ▴ 10
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DESeq2 for Ribosomal profiling analysis [two-factor designs]
deseq2 ribosome profiling
updated 3.2 years ago by 34k • written 3.2 years ago by ▴ 10
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Problem in reading .bam files (aligned to transcriptome) with ribofileCR function
R riboseqr ribosome profiling
3.6 years ago bsad • 0
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How to not include start region in analyzing ribosome profiling data?
riboprofiling ribosome profiling
4.1 years ago nicholsonangela7 • 0
3
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974
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Extracting Coordinates of startcodon from Grangeslist
biomart bioconductor grangeslist cds ribosome profiling
updated 4.3 years ago by 15k • written 4.3 years ago by ▴ 10
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DESeq2 for translation efficiency when there are normalization issues
deseq2 translation efficiency spikes ribosome profiling
4.9 years ago GFM ▴ 20
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error in frameCounting in riboSeqR
riboseqr ribosome profiling
updated 5.5 years ago by ▴ 180 • written 5.6 years ago by • 0
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error in callingFrames : riboSeqR
R riboseqr ribosome profiling
5.9 years ago ohtack9 • 0
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ribosome profiling analysis with different dispersions
deseq2 linear model ribosome profiling stats
updated 6.1 years ago by 7.6k • written 6.1 years ago by ▴ 90
12 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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