User: Vang Le

gravatar for Vang Le
Vang Le70
Reputation:
70
Status:
Trusted
Location:
Denmark
Last seen:
1 month, 3 weeks ago
Joined:
4 years, 2 months ago
Email:
v**@rn.dk

Posts by Vang Le

<prev • 21 results • page 1 of 3 • next >
0
votes
1
answers
81
views
1
answers
Comment: C: Homo.sapiens package: Some genes are not found
... Hi James. I made update to the question. Please take a look from "Update with additional information. " downward. ...
written 9 weeks ago by Vang Le70
0
votes
1
answers
81
views
1
answers
Comment: C: Homo.sapiens package: Some genes are not found
... Thank you for this James. Using your approach, I could reduce number of missing genes to 400 now. Of these 400, I check some and found out that they are partially overlapped with hg19.knownGene. It seems that they use ensembl gene coordinate, with HGNC symbol. How do I use (sort of) TxDb ensGene ins ...
written 9 weeks ago by Vang Le70
1
vote
1
answer
81
views
1
answer
Homo.sapiens package: Some genes are not found
... I have a long list of about 700 genes. Some of them here: ABCF1 ABHD16A ACYP1 ADAMTSL4-AS1 AGER AGPAT1 AIF1 AKAP17A ALPI AMY1A ANKRD20A1 ANKRD20A3 ANKRD42 ANKRD60 APOM ARHGAP27 ARL17A ARPP19 ASMT ASMTL ATAT1 ATF6B ATP6V1G2-DDX39B AUNIP AZIN1-AS1 B3GALT4 BAG6 BECN2 BLACE BMS1P18 BPY2 BRD2 BTNL10 BT ...
homo.sapiens written 10 weeks ago by Vang Le70
0
votes
1
answers
94
views
1
answers
Comment: C: AnnotationHub, force update snapshot date?
... Not possible to upgrade to R 3.5 now, but I believe it will solve the problem as you suggested. Thanks   ...
written 3 months ago by Vang Le70
1
vote
1
answer
94
views
1
answer
AnnotationHub, force update snapshot date?
... Somehow I can't get the latest date: > library(AnnotationHub) > ah <- AnnotationHub() snapshotDate(): 2017-10-27 > query(ah, c("norvegicus", "release-92")) AnnotationHub with 0 records # snapshotDate(): 2017-10-27 Is there cache data somewhere that I need to delete? > sessionInf ...
annotationhub written 3 months ago by Vang Le70 • updated 3 months ago by shepherl ♦♦ 830
0
votes
0
answers
96
views
0
answers
Comment: C: 'downstream' disappeared from GenomicRanges package?
... Thank you Martin. I will look into that function but I am hesitated to use it before finding some better solution. This is because I don't work anything with variants for this data. Can follow or precede do the job? ...
written 3 months ago by Vang Le70
0
votes
0
answers
96
views
0
answers
'downstream' disappeared from GenomicRanges package?
... I have a legacy script using `downstream` function which I believe it is from GenomicRanges package. I may be wrong, then I would like to know the correct package to use. I found out about this after updating to bioconductor version 3.6 (see full sessioninfo below). > sessionInfo() R version 3. ...
genomicranges written 3 months ago by Vang Le70
0
votes
0
answers
476
views
0
answers
Job: Bioinformatician in Aalborg University Hospital, Denmark
... Aalborg University Hospital Section of Molecular Diagnostics We are looking for a motivated bioinformatician to strengthen and expand bioinformatic work force in response to increasing needs of a molecular diagnostic group utilizing big data. Application deadline: 19th of April 2017 Core tasks D ...
job bioinformatician job written 19 months ago by Vang Le70
0
votes
1
answer
331
views
1
answer
count coverage for exact matches to sequence pattern
... I have BSgenome hg19, a GTF file containing gene coordinates, and a BAM file. This is what I want to do: 1. Search for all occurrences of my sequence, and save the coordinates in a range objects. Following is the current implementation, but the output found coordinates are based on the first bases ...
genomicfeatures rsamtools written 21 months ago by Vang Le70 • updated 21 months ago by Michael Lawrence10k
0
votes
1
answers
2.1k
views
1
answers
Comment: C: resize (shrink/expand) GenomicRanges
... I want to do the same thing, like to include promoter regions (2kb upstream) to my genes. I wonder what is the reasons for not having this feature in GenomicRanges package until now? I was also trying to use `resize` function for this purpose. Luckily I found this thread. ...
written 22 months ago by Vang Le70

Latest awards to Vang Le

Popular Question 19 months ago, created a question with more than 1,000 views. For extract chromosomes and read-starts from a BAM file to a data.frame?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 379 users visited in the last hour