User: aatsmith

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aatsmith0
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Posts by aatsmith

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Comment: C: error in SRAdb
... I received a reply from Jack Zhu for SRAdb and from Rick Lapoint for the SRA. I'm copying the essence of those answers here: this error is common when the SRAdb package version is out-of-date. (in my case this is because my R version is out-of-date, which is in turn due to my operating system be ...
written 14 days ago by aatsmith0
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Comment: C: error in SRAdb
... I am having the same problem too. By modifying the getSRAdbFile() function a bit, I've noticed that none of the 3 SQLite backup GZ files are available. I will email the maintainers.   By the way: the previous SRAdb version returned ByExp FTP addresses for the SRA files, however the NCBI SRA's "ByE ...
written 15 days ago by aatsmith0
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DESeq2 feature request: parallelised refitWithoutOutliers()
... Dear DESeq2 team,   I am currently using DESeq2 (v1.12.0 under R 3.3.0) to analyse some processed single-cell RNA-seq data, and the data's inherent noisiness is leading to many genes having many values detected as outliers (eg >3k genes out of 10k analysed). Given the number of samples (cells, ...
deseq2 written 18 months ago by aatsmith0 • updated 18 months ago by Michael Love15k
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Answer: A: scran: question on minimum cluster size for computeSumFactors()
... Hi Aaron, Thank you for your prompt reply & your insight! I have between 80 & 96 cells in each sub-population, for a total of less than 280, so that sounds borderline as you said, but worth a try - especially since it can hardly be worse than the traditional normalisation methods. I've bee ...
written 18 months ago by aatsmith0
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scran: question on minimum cluster size for computeSumFactors()
... Dear Bioconductor support,   We are currently considering using Bioconductor package scran to analyse some publicly-available single-cell RNA-seq data (quantified at the transcript level with Kallisto, aggregated to gene level with tximport). This dataset has (after QC) less than 90 cells in each ...
normalization clustering single cell scran written 19 months ago by aatsmith0

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