User: eric.blanc

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eric.blanc0
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Posts by eric.blanc

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Comment: C: tximeta link to transcriptome
... Thanks for your answer, it makes perfect sense, and everything's working now. One last comment if I may: the private function `tximeta:::getMetaInfo` appears to assume that salmon's `--auxDir` argument shouldn't be used (the `aux_info` default value is the only path compatible with `tximeta`). I m ...
written 4 weeks ago by eric.blanc0
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tximeta link to transcriptome
... Hi, I have troubles with using tximeta from the sample table (`Cov` below). I loaded the sample table (3 columns, names (all unique), files (absolute paths to `quant.sf`) & condition (all "A")). I have created a linked transcriptome from downloaded files using: ``` makeLinkedTxome( indexD ...
deseq2 written 4 weeks ago by eric.blanc0 • updated 4 weeks ago by Michael Love26k
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biomaRt::getBM fails with "Error in scan"
... Hi, I'm using `biomaRt` to extract from ENSEMBL amino-acid sequences together with the APPRIS transcript status. I am using the `getBM` function, as I couldn't find a way to add the APPRIS status using `getSequence`. However, I get an error when I request (beside the sequence) both the SwissProt ID ...
biomart written 8 months ago by eric.blanc0 • updated 8 months ago by Mike Smith4.0k
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Comment: C: deseq2 DESeqDataSet size when saved
... Thanks Michael, and sorry I wasn't able to find the relevant thread...   ...
written 13 months ago by eric.blanc0
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deseq2 DESeqDataSet size when saved
... Hi, I am trying to generate small files to include in my package for regression tests. One of them is a small DESeqDataSet object (object dds_small below, the first 50 features from a complete analysis store in object dds). However, when I save the small object, its size remains very large: > ...
infrastructure deseq2 importing deseqdataset written 13 months ago by eric.blanc0 • updated 13 months ago by Michael Love26k

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