User: Kyle Johnsen

gravatar for Kyle Johnsen
Kyle Johnsen20
Reputation:
20
Status:
New User
Location:
United States/Brigham Young University
Last seen:
3 months, 3 weeks ago
Joined:
2 years, 9 months ago
Email:
j************@gmail.com

Posts by Kyle Johnsen

<prev • 19 results • page 2 of 2 • next >
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Can't access devel version of ExperimentHub in Travis CI
... I use Travis CI for developing my Bioconductor package, and it's been working well so far. But now that I rely on ExperimentHub (and new data in ExperimentHub at that), I'm running into problems getting the most recent snapshots. I'm using the bioc-devel option in the .travis.yml file, and in the lo ...
continuous-integration experimenthub written 8 months ago by Kyle Johnsen20
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Comment: C: BiocManager::install() breaks; can't install bioc-devel
... This: source("https://bioconductor.org/biocLite.R") biocLite() ...
written 9 months ago by Kyle Johnsen20
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Answer: A: BiocManager::install() breaks; can't install bioc-devel
... I installed Bioconductor first, and then it worked. I didn't know Bioconductor needed to already be installed. ...
written 9 months ago by Kyle Johnsen20
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BiocManager::install() breaks; can't install bioc-devel
... BiocManger::install(version='devel') doesn't work for me. This is what happens: > BiocManager::install(version = 'devel') Error: $ operator is invalid for atomic vectors   I was able to identify the problem on line 23 of the install package, when .instal ...
installation biocmanager written 9 months ago by Kyle Johnsen20
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What is the function of the 'make-metadata.R' script when making a ExperimentHub package?
... As I begin writing the make-metadata.R script, I'm not sure as to its purpose. Is it supposed to make my life easier by grabbing programmatically things like modification dates, MD5 sums, and such? (In which case it would only work on my machine, where I have access to the files locally.) Or should ...
experimenthub written 9 months ago by Kyle Johnsen20 • updated 9 months ago by shepherl ♦♦ 1.4k
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Comment: C: Can I create a GmapGenome with a relative file path?
... Great, thank you! ...
written 2.1 years ago by Kyle Johnsen20
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Comment: C: Can I create a GmapGenome with a relative file path?
... Yes it does ...
written 2.1 years ago by Kyle Johnsen20
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Can I create a GmapGenome with a relative file path?
... I'm developing a package which uses a GmapGenome in calling variants, and therefore am trying to create a small GmapGenome (out of a fasta file for just one chromosome) in my unit tests. The problem I run into, however, is that GmapGenome seems not to work for relative file paths. I confirmed this ...
gmapr gmapgenome fastafile written 2.1 years ago by Kyle Johnsen20 • updated 2.1 years ago by Michael Lawrence11k
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Using GRanges and IRanges to simply get all chromosome data
... Hi! I have basically two questions. I'm trying to analyze RNA-seq data, contained in BAM files, using applyPileups. The ApplyPileupsParam, however, needs the 'which' paremeter, which needs a GRanges object. Is there an easy way to, say, get all chromosomes from a file (not contigs)? And since it ...
iranges granges written 2.8 years ago by Kyle Johnsen20 • updated 2.8 years ago by Martin Morgan ♦♦ 23k

Latest awards to Kyle Johnsen

Scholar 9 months ago, created an answer that has been accepted. For A: Can't access devel version of ExperimentHub in Travis CI
Scholar 9 months ago, created an answer that has been accepted. For A: Strange problem in example check of package

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