User: jessica.hekman

Reputation:
40
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New User
Location:
United States
Last seen:
3 years, 9 months ago
Joined:
4 years, 8 months ago
Email:
j*************@gmail.com

Posts by jessica.hekman

<prev • 60 results • page 1 of 6 • next >
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Comment: C: bumphunter::annotateNearest with non-human genome
... Amazing that it took me this long to get back to this! (In the meantime I went to Siberia, passed my prelims, presented my research twice. and helped submit an NSF proposal... All of which prevented me from getting to my own research.) Anyways: It works! Thanks again to Leo and Rafa for your suppor ...
written 3.8 years ago by jessica.hekman40
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Comment: C: sqliteSendQuery in AnnotationDbi
... Ah, thank you! Yes, I'll go change that now. ...
written 4.0 years ago by jessica.hekman40
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Answer: A: sqliteSendQuery in AnnotationDbi
... The solution was: library("AnnotationDbi") library("biomaRt") library("GenomicFeatures") dogTxDb <- makeTxDbFromBiomart(biomart="ensembl", dataset="cfamiliaris_gene_ensembl", transcript_ids=NULL, circ_s ...
written 4.0 years ago by jessica.hekman40
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Comment: C: sqliteSendQuery in AnnotationDbi
... Thanks James! Martin: yeah, I do intend to create a dog transcripts package at some point, but first I just wanted to make sure everything worked as expected. (I will also admit that I'm nervous about sharing a package with others as I'm still pretty new to Bioconductor, but I suppose I need to suc ...
written 4.0 years ago by jessica.hekman40
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Comment: C: sqliteSendQuery in AnnotationDbi
... Sorry -- dogTxEnsembl.rda contains dogTx which was built like so: dogTx <- makeTranscriptDbFromBiomart(biomart="ensembl", dataset="cfamiliaris_gene_ensembl", transcript_ids=NULL, circ_seqs=DEFAULT ...
written 4.0 years ago by jessica.hekman40
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sqliteSendQuery in AnnotationDbi
... HI all. I am trying to run derfinder, but am running into a problem with its calls to AnnotationDbi. I seem to have isolated the problem like so: > library ("AnnotationDbi") > load("dogTxEnsembl.Rda") > class(dogTx) [1] "GenomicFeatures" > organism(dogTx) Error in sqliteSendQuery(con, ...
annotationdbi written 4.0 years ago by jessica.hekman40
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Comment: C: derfinder: analyzeChr() freezes in f-stat calculation
... Loopback, not lookback. ...
written 4.2 years ago by jessica.hekman40
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Comment: C: derfinder: analyzeChr() freezes in f-stat calculation
... OK! I contacted my sysadmin for help in finding an appropriate port to use with R_PARALLEL_PORT, and he said "oh, looks like loopback is blocked -- I opened it back up, see if things work now." And now they do. So the answer is: check loopback and make sure it's open. Thanks to both of you for all ...
written 4.2 years ago by jessica.hekman40
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Comment: C: derfinder: analyzeChr() freezes in f-stat calculation
... That's so helpful, thanks! I'm going to be out of the country for a week starting today, but when I get back I'll sit down and try to figure this out. I'll post whatever I find here (hopefully an answer about what ports to open, for the benefit of future answer seekers). ...
written 4.2 years ago by jessica.hekman40
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Comment: C: derfinder: analyzeChr() freezes in f-stat calculation
... I just installed 3.2: R version 3.2.0 alpha (2015-03-26 r68103). In a new session with nothing loaded:   > x <- parallel::mclapply(1:10, sqrt) > cl <- parallel::makeCluster(2, "PSOCK") Again parallel:makeCluster() hung and I had to exit with ^C. I conclude that 3.2 vs 3.3 isn't the ...
written 4.2 years ago by jessica.hekman40

Latest awards to jessica.hekman

Popular Question 3.8 years ago, created a question with more than 1,000 views. For derfinder: analyzeChr() breaks on chromosomes > 22
Supporter 3.8 years ago, voted at least 25 times.

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