User: Chao-Jen Wong

gravatar for Chao-Jen Wong
Reputation:
30
Status:
New User
Location:
USA/Seattle/Fred Hutchinson Cancer Research Center
Last seen:
6 months ago
Joined:
4 years, 5 months ago
Email:
c****@fredhutch.org

Posts by Chao-Jen Wong

<prev • 34 results • page 2 of 4 • next >
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Comment: C: GenomicAlignment::pintersect() of two overlapping ranges - CIGAR is empty after
... The results if using R/devel & Bioconductor 3.4.   > sessionInfo() R Under development (unstable) (2016-12-19 r71815) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 14.04.3 LTS locale:  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_ ...
written 2.3 years ago by Chao-Jen Wong30
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GenomicAlignment::pintersect() of two overlapping ranges - CIGAR is empty after narrowing
... Hi guys,  My task is to find the width of intersect areas of GAlignments reads and GRanges objects. First, I have made sure that there are overlapping for at least 1L by using findOverlaps() and then use pintersect() and width() to find the width of the overlapping area. For my case, I have a splic ...
genomicalignments written 2.3 years ago by Chao-Jen Wong30 • updated 2.3 years ago by Michael Lawrence11k
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Comment: C: keepSeqlevels for GRangesList: drop elements with multiple seqnames
... Thanks a lot for making the changes!  ...
written 2.3 years ago by Chao-Jen Wong30
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Comment: C: Bioconductor packages for machine learning with RNAseq
... There is a bioconductor package "MLInterfaces" that contains interfaces to R machine learning procedures such as svm, random forest, knn, and etc.  Those procedures are built for general purpose, yet you might find it quite helpful for expression data. ...
written 2.5 years ago by Chao-Jen Wong30
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keepSeqlevels for GRangesList: drop elements with multiple seqnames
... Hi, I have usually used keepSeqlevels() to subset the list of transcript or exon (GRangesList built by transciptBy() and exonsBy()) and keep the transcripts of interest. Not until recently did I find out that many of genes that I am interested in are missing after using keepSeqlevels() and those mis ...
genomeinfodb keepseqlevels written 2.5 years ago by Chao-Jen Wong30 • updated 2.4 years ago by Valerie Obenchain6.7k
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Comment: C: problems with GenomicFeatures::supportedUCSCtables("hg38")
... Thank you, Valerie and Herve. ...
written 2.5 years ago by Chao-Jen Wong30
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problems with GenomicFeatures::supportedUCSCtables("hg38")
... The UCSC Genome browser have updated GENCODE track to v24 and track "GENCODE v22" is not longer supported. This affects makeTxDbFromUCSC() and makeTxDbPackageFromUCSC() that depend on supportedUCSCtables("hg38"). So using the current GenomicFeature v1.24.5 on R 3.3 or R3.4, we have > supported ...
genomicfeatures written 2.6 years ago by Chao-Jen Wong30 • updated 2.5 years ago by Valerie Obenchain6.7k
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Comment: C: supportedUCSCtables(genome="hg38"): Is ensGene track really available?
... Thanks, Herve. browseUCSCtrack() is very helpful!!!! ...
written 2.9 years ago by Chao-Jen Wong30
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supportedUCSCtables(genome="hg38"): Is ensGene track really available?
... Hi, I was using supportedUCSCtables() to find what tracks are available  on UCSC genome browser and found the function is a bit mis-leading. The "ensGene" is in deed available on hg19 genome, but not on hg38. So when I do the following, I would get errors. I then use rtracklayer::trackName() to fin ...
genomicfeatures written 3.0 years ago by Chao-Jen Wong30 • updated 3.0 years ago by Hervé Pagès ♦♦ 13k
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Comment: C: DESeq2::rlog - does it make sense to use it when I don't have duplicates?
... Thanks, Michael. It is good to know that setting blind=TRUE leads to design=~1. I don't recall seeing it on the man page.  ...
written 3.0 years ago by Chao-Jen Wong30

Latest awards to Chao-Jen Wong

Scholar 3.1 years ago, created an answer that has been accepted. For A: Combining .idat and GEO data sets in minfi

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