User: felix.ernst

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Posts by felix.ernst

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Answer: A: rtracklayer demo bug
... Thanks a lot.   ...
written 9 weeks ago by felix.ernst0
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rtracklayer demo bug
... Hello, does anyone else have a problem using demo(targets) to have a look at the example in the rtracklayer package? The error is given after chunk 6 > view <- browserView(session, range, + hide = c("refGene", "mgcFullMrna", "intronEst"), + dense = " ...
rtracklayer written 9 weeks ago by felix.ernst0
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Comment: C: intronsByTranscript and fiveUTRsByTranscript - not recognized annotations
... TxDb expects UTR regions to be included in the exon annotation. Reminder: exon != CDS ...
written 3 months ago by felix.ernst0
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Comment: C: intronsByTranscript and fiveUTRsByTranscript - not recognized annotations
... Thanks Michael. I checked again, You are right :/ :( ...
written 3 months ago by felix.ernst0
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Comment: C: intronsByTranscript and fiveUTRsByTranscript - not recognized annotations
... > exonsBy(txdb) GRangesList object of length 1: $1 GRanges object with 2 ranges and 3 metadata columns: seqnames ranges strand | exon_id exon_name exon_rank <Rle> <IRanges> <Rle> | <integer> <character> <integer> [1] chr ...
written 3 months ago by felix.ernst0
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(Closed) intronsByTranscript and fiveUTRsByTranscript - not recognized annotations
... Hi, I am having a bit of trouble to get the introns and exons from a transcript. Have a look at this snippet. library(GenomicFeatures) file <- "test.gff3" print(readLines(file)) txdb <- makeTxDbFromGFF(file) print(transcripts(txdb)) print(intronsByTranscript(txdb)) print(fiveUTRsByTranscr ...
genomicfeatures written 3 months ago by felix.ernst0 • updated 3 months ago by Michael Lawrence10.0k
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seqnames versus chrom
... Dear all, I can retrieve the chromosome names stored in a GRanges object either using GenomeInfoDb::seqnames() or rtracklayer::chrom(). This deviates from the use of the other accessor functions, such as BiocGenerics::start(), BiocGenerics::end(), etc Is there a reason for this split up? Is there ...
rtracklayer genomeinfodb biocgen written 4 months ago by felix.ernst0 • updated 4 months ago by Michael Lawrence10.0k
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Comment: C: Correct way to load a package inside bplapply function
... Sorry, forgot that. I update the sessionInfo output in the original thread opening post, since there is a 5000 character limit for replies. ​the dependencies can be installed using this: source("https://bioconductor.org/biocLite.R") biocLite() biocLite("devtools") devtools::find_rtools() library(de ...
written 9 months ago by felix.ernst0
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Comment: C: Correct way to load a package inside bplapply function
... addition because of the 5000 spaces limit: The output is of course much shorter and for each file loaded the output appears: <environment: namespace:base> cpu elapsed transient class <environment: namespace:tools> ...
written 9 months ago by felix.ernst0
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Comment: C: Correct way to load a package inside bplapply function
... The problem exists with 3.4.1 in a fresh install as well. The example function does not return a output, so the problem has to be in connection with some thing else. Therefore I modified the function stepwise and commented out all the function calls and simplified some stuff so I ended up with this ...
written 9 months ago by felix.ernst0

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