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branchpointer
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Predict branchpoints closer to the 3' splice site
branchpointer
2.1 years ago
Matthias Lienhard
▴ 240
0
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1
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619
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Branchpointer issues with chromosome names and getListElement(x, i, ...)
branchpointer
updated 17 months ago by
kiran
• 0 • written 2.2 years ago by
alexandre.maucuer
• 0
0
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1
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851
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branchpointer: trouble to read gtf
gtfToExons
"Error:subscriptcontainsinvalidnames"
gtf
branchpointer
updated 2.6 years ago by
b.signal
• 0 • written 2.6 years ago by
frank.maiwald
• 0
0
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0
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882
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branchpointer ERROR: Error in data.table::fread(paste0(workingDirectory, "/mutation_", uniqueId, :
branchpointer
6.3 years ago
noah.pieta
• 0
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Comment: How to retrieve gene ontology GO class from gene list?
by
bandconductor
• 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions
by
JKim
• 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
James W. MacDonald
65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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