User: foehn

gravatar for foehn
foehn10
Reputation:
10
Status:
New User
Location:
Last seen:
2 days, 19 hours ago
Joined:
6 months, 4 weeks ago
Email:
f****@foxmail.com

Posts by foehn

<prev • 12 results • page 1 of 2 • next >
1
vote
1
answer
35
views
1
answer
rtracklayer BigBed format
... Hello, In this tutorial (https://kasperdanielhansen.github.io/genbioconductor/html/rtracklayer_Import.html), it appears that rtracklayer should be able to handle BigBed ("...includes functionality for parsing file formats associated the UCSC Genome Browser such as BED, Wig, BigBed and BigWig"). ...
rtracklayer ngs bigbed written 10 days ago by foehn10 • updated 10 days ago by Michael Lawrence10k
4
votes
2
answers
115
views
2
answers
Speed efficient way to select the n-th element from GRangsList
... Hello, Suppose we have a simple task, that is, to select the fifth range from each GRanges object from a GRangesList object. I can think of two methods: library(EnsDb.Hsapiens.v86) library(microbenchmark) X <- exonsBy(EnsDb.Hsapiens.v86, by = "tx") X <- X[lengths(X) > 10] # to make sure ...
iranges genomicranges R written 4 weeks ago by foehn10
0
votes
1
answer
111
views
1
answers
Comment: C: rtracklayer cannot export empty BED file
... OK, got you, thanks. ...
written 8 weeks ago by foehn10
0
votes
1
answer
111
views
1
answers
Comment: C: rtracklayer cannot export empty BED file
... Just tried out v1.43.0 from bioc v3.9 (devel, which depends on R 3.6). Unfortunately it didn't work... > export(GRanges(), con = "test.bed") Error in `$<-.data.frame`(`*tmp*`, score, value = 0) : replacement has 1 row, data has 0 > sessionInfo() R Under development (unstable) (2018-11-1 ...
written 8 weeks ago by foehn10
0
votes
1
answer
111
views
1
answers
Comment: C: rtracklayer cannot export empty BED file
... Thanks for prompt reply. The current release version is 1.42.0 and devel version 1.43.0. Does it mean I need to install from the devel channel? ...
written 8 weeks ago by foehn10
0
votes
1
answer
111
views
1
answer
rtracklayer cannot export empty BED file
... Hello, I found one issue with rtracklayer's export.bed function. It seems that it cannot export an empty GRanges object. For example, > export(GRanges(), con = "test.bed") Error in `$<-.data.frame`(`*tmp*`, "score", value = 0) : replacement has 1 row, data has 0 > sessionInfo() R versi ...
rtracklayer genomicranges bed written 8 weeks ago by foehn10 • updated 8 weeks ago by Michael Lawrence10k
0
votes
0
answers
137
views
0
answers
Comment: C: mitochodria isCircular equals to FALSE in EnsDb.Hsapiens.v86 and EnsDb.Mmusculus
... Got it. Thanks for probing into this issue. ...
written 11 weeks ago by foehn10
0
votes
0
answers
137
views
0
answers
Comment: C: mitochodria isCircular equals to FALSE in EnsDb.Hsapiens.v86 and EnsDb.Mmusculus
... Thanks a lot @Johannes! ...
written 11 weeks ago by foehn10
0
votes
0
answers
137
views
0
answers
mitochodria isCircular equals to FALSE in EnsDb.Hsapiens.v86 and EnsDb.Mmusculus.v79
... Hi there, I'm using R annotation packages EnsDb.Hsapiens.v86 and  EnsDb.Mmusculus.v79. I notice that both of them annotate mitochondrial DNA to non-circular, which seems contrary to the biology > as.data.frame(seqinfo(EnsDb.Hsapiens.v86))["M", ] seqlengths isCircular genome MT 16569 ...
annotation R ensembldb written 11 weeks ago by foehn10
0
votes
1
answer
313
views
1
answers
Comment: C: an error in BioMart regarding gene annotations
... Any news about package update? Thanks. ...
written 5 months ago by foehn10

Latest awards to foehn

No awards yet. Soon to come :-)

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 263 users visited in the last hour