User: Chao-Jen Wong

gravatar for Chao-Jen Wong
Reputation:
30
Status:
New User
Location:
USA/Seattle/Fred Hutchinson Cancer Research Center
Last seen:
4 months, 1 week ago
Joined:
2 years, 8 months ago
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c****@fredhutch.org

Posts by Chao-Jen Wong

<prev • 30 results • page 1 of 3 • next >
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Comment: C: Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
... Thanks a lot. I did not know that. ha...... ...
written 4 months ago by Chao-Jen Wong30
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Comment: C: Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
... FYI, I use makeTxDbFromBiomart() instead and get the right gene IDs and transcripts. However, the metadata was wrong due to error detected by .Ensembl_getMySQLCoreDir(), which is not a big deal. sessionInfo() is the same as above. Thanks.   > txdb <- makeTxDbFromBiomart(biomart="ENSEMBL_MAR ...
written 4 months ago by Chao-Jen Wong30
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Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
... As I was using the TxDb.Mmusculus.UCSC.mm10.ensGene package installed using biocLite(), the ID appears to be neither Eensembl ID nor EntrezID. I believe those gene IDs are wrong. (I am using Bioconductor 3.5 on R/3.4, and all the packages are just updated. see sessionInfo() below.) > library(Tx ...
genomicfeatures txdb written 4 months ago by Chao-Jen Wong30 • updated 4 months ago by James W. MacDonald43k
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Comment: C: How to clip a sequence (DNAStringSet) using narrow() and keep the wanted sequenc
... Hi, Michael, I just pileup() and it seems to work for my purpose. I parse the return the data.frame of pileup() and compare with the reference genome to define the type of mismatch.  I have not tried tallyVariants(), but it sounds even better. I will definitely try it tomorrow.  Thanks for the help ...
written 6 months ago by Chao-Jen Wong30
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How to clip a sequence (DNAStringSet) using narrow() and keep the wanted sequence?
... Hi, bioconductor members,  I have two questions here. The first one is basically about how to use narrow() to keep the wanted sequence in an efficient way. I have a read and corresponding cigar, a subset from my GAlignments instance. I want to clip the insertion and soft-clip from the read so that ...
genomicalignments narrow mismatch written 6 months ago by Chao-Jen Wong30
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Comment: C: GenomicAlignment::pintersect() of two overlapping ranges - CIGAR is empty after
... Thank you, Michael, for the helpful details. Converting with grglist() using drop.D.ranges=TRUE before calling findoverlaps() would definitely work for my case. Wouldn't have known this before.    Thanks, CJ   ...
written 6 months ago by Chao-Jen Wong30
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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 7 months 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 7 months ago by Chao-Jen Wong30 • updated 7 months ago by Michael Lawrence9.3k
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Comment: C: keepSeqlevels for GRangesList: drop elements with multiple seqnames
... Thanks a lot for making the changes!  ...
written 7 months 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 8 months ago by Chao-Jen Wong30

Latest awards to Chao-Jen Wong

Scholar 15 months ago, created an answer that has been accepted. For A: Combining .idat and GEO data sets in minfi

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