Showing : SRA • reset
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Creating a DESeqDataSet from a RangedSummarizedExperiment - where is the design parameter in RangedSummarizedExperiment
SRA DESeq2
4.6 years ago Serge • 0
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1.4k
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Problem for Splitting reverse and forward reading in my RNA-seq
RNA-seq SRA reverse reads forward reads
7.6 years ago modarzi ▴ 10
2
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1
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1.9k
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Uniting SRA Data into a single file
R fastq SRA sradb
updated 9.2 years ago by 25k • written 9.2 years ago by • 0
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3
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4.7k
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download SRR*.lite.sra files using fastq-dump command
sra chipseqDB fastq-dump .lite.sra
updated 9.3 years ago by 68k • written 9.3 years ago by • 0
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1.9k
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Search SRA based on BioSample Attributes
ncbi sra search
10.0 years ago massacomgrao • 0
6
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4.6k
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Tutorial: Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
rnaseq biocparallel workflows sra Tutorial
10.5 years ago Sean Davis 21k
6 results • Page 1 of 1
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Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
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…
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A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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
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