User: dario.beraldi

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Posts by dario.beraldi

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Comment: C: bug in "dispersion" argument in edgeR - rpkmByGroup
... Hi Gordon- Thanks for quick reply, as always! About versions, I installed edgeR via conda/bioconda using `conda install bioconductor-edger=3.26.0`. It appears that the bioconda recipe for version 3.26.0 ([here](https://github.com/bioconda/bioconda-recipes/blob/197f0880f95879037da5822c95141e685b00b48 ...
written 5 months ago by dario.beraldi0
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bug in "dispersion" argument in edgeR - rpkmByGroup
... Hi- Trying to run the `rpkmByGroup` function from edgeR, I get the error below. rpkmByGroup(y, gene.length= rep(1000, nrow(y))) Error in cpmByGroup.default(y = y, group = group, dispersion = dispersion, : formal argument "dispersion" matched by multiple actual arguments I think i ...
edger rpkm written 5 months ago by dario.beraldi0 • updated 5 months ago by rosehahn85830
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Shearwater missing variant
... Hello, I'm using Shearwater in the deepSNV package to detect variants. I'm trying to understand why some variants are missed even they seem quite clear from manual inspection. Here's a VCF record as an example: chr18   5041382 .   A   C   1   PASS    ER=0.142;PI=0.5;AF=0.5;LEN=1    GT:GQ:BF:VF:FW: ...
deepsnv shearwater variant written 23 months ago by dario.beraldi0
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Comment: C: SRAdb: could not find function "sqliteTableFields"
... Done. Thanks a lot that fixed it! ...
written 5.0 years ago by dario.beraldi0
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SRAdb: could not find function "sqliteTableFields"
... Hello, I just installed SRAdb. I get the error "could not find function "sqliteTableFields" when executing getSRA. Any idea what's wrong? Many thanks! Dario library(SRAdb) sra_dbname <- 'SRAmetadb.sqlite' sra_con <- dbConnect(dbDriver("SQLite"), sra_dbname) rs <- getSRA (search_t ...
sradb sqlite written 5.0 years ago by dario.beraldi0 • updated 5.0 years ago by Sean Davis21k

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Popular Question 22 months ago, created a question with more than 1,000 views. For SRAdb: could not find function "sqliteTableFields"

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