User: Sonali Arora

gravatar for Sonali Arora
Sonali Arora350
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350
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United States
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1 year ago
Joined:
2 years, 11 months ago
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s*****@fhcrc.org

Posts by Sonali Arora

<prev • 21 results • page 1 of 3 • next >
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Answer: A: Normal Patient Samples from GSE62944
... Hi Hamda, Solution #1 Please see the supplementary file section for  the GEO page  -we have added only the   7706 tumor samples from TCGA - the Normal samples have not been added.  > library(AnnotationHub) > ah = AnnotationHub() > ah <- query(ah , "GSE62944") > data <- ah[["AH2 ...
written 12 months ago by Sonali Arora350
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Comment: C: error in callingFrames : riboSeqR
... Hi Tak, I faced a similar issue just yesterday with Human Data - but I raised it on bioc-devel.. should have probably posted it here -  Here is a link to that discussion -  https://stat.ethz.ch/pipermail/bioc-devel/2015-October/008246.html Hope that helps! Sonali.    ...
written 18 months ago by Sonali Arora350
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Answer: A: biomaRt fails for M.musculus annotation, Ensembl version 80
... Hi Sarah, An alternate way of annotating your Ensembl gene would be to use the Bioconductor package AnnotationHub.  It contains gtf files from Ensembl release 69 to 81 for all organisms released by Ensembl.  The data is presented as GRanges which can easily be manipulated to get information about ...
written 19 months ago by Sonali Arora350
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News: Gencode GFF3 and FASTA files now available via AnnotationHub
... GFF3 and FASTA files from the latest release of  Gencode  are now available via AnnotationHub. (biocVersion 3.2 only)  One can access GFF3 and FASTA files from the latest release of Homo sapiens (release 23) using the following code snippet : > library(AnnotationHub) > ah = AnnotationHub() ...
annotationhub news fasta gencode gff3 written 20 months ago by Sonali Arora350
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Answer: A: possible conflict between renameSeqLevels (TxDb) and isActiveSeq (TxDb)
... Hi Robert,  My Understanding is that you're trying to do the following 1) make a TranscriptDb from UCSC for the ref gene table 2) obtain exons for chr 1-25,X,Y,M  Firstly, makeTranscriptDbFromUCSC is defunct - Please use makeTxDbFromUCSC instead. > refSeqDb3 = suppressWarnings (makeTxDbFromU ...
written 20 months ago by Sonali Arora350
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Tutorial: Course Material from BioC 2015: Where Software and Biology Connect
... Course material from BioC 2015: Where Software and Biology Connect now available through the Bioconductor Courses & Conferences and github. Material from Developer Day and workshops now added.    ...
course-material bioc2015 tutorial written 21 months ago by Sonali Arora350 • updated 21 months ago by Dan Tenenbaum ♦♦ 8.1k
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Answer: A: Ensembl release 81 is out!
... We have added the GTF files from Ensembl's release-81 to Bioconductor (Bioc version 3.1 and 3.2). You can access them via AnnotationHub:  > library(AnnotationHub) > ah = AnnotationHub() snapshotDate(): 2015-07-17 > gtf_hs_81 <- query(ah, c("ensembl","gtf", "81", "homo sapiens")) > ...
written 21 months ago by Sonali Arora350
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Answer: A: RNA-seq analysis with R/BioC: alignment and read counts
... Hi Fiona,  My understanding from the information that you've given is, that the seqlevelsStyle of the GFF files is not UCSC and that is giving rise to these issues. I suggest using the following steps  a) read in the GFF file as a GRanges b) read in one of the bam files as a GenomicAlignments.  c) ...
written 21 months ago by Sonali Arora350
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Tutorial: Epigenomics RoadMap Project files now accessible via AnnotationHub
... Files from Epigenomics RoadMap Project have been added to AnnotationHub. This vignette inside AnnotationHub gives you a quick tour on how to access these files  via the Hub with some examples. Please let us know if you'd like any other files to be added to the Hub from the same project or another. ...
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Answer: A: Ensembl release 80 is out!
... We have added the GTF files from Ensembl's release-80 to Bioconductor (Bioc version 3.1 and 3.2) . You can access  them :  > library(AnnotationHub) > ah = AnnotationHub() > gtf = query(ah , c("gtf", "80", "Ensembl", "rattus")) > gtf # access the record information AnnotationHub wi ...
written 23 months ago by Sonali Arora350

Latest awards to Sonali Arora

Scholar 12 months ago, created an answer that has been accepted. For A: Normal Patient Samples from GSE62944
Popular Question 12 months ago, created a question with more than 1,000 views. For Course Material from BioC 2015: Where Software and Biology Connect
Popular Question 12 months ago, created a question with more than 1,000 views. For Epigenomics RoadMap Project files now accessible via AnnotationHub
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Ensembl release 80 is out!
Appreciated 21 months ago, created a post with more than 5 votes. For Epigenomics RoadMap Project files now accessible via AnnotationHub
Appreciated 23 months ago, created a post with more than 5 votes. For Epigenomics RoadMap Project files now accessible via AnnotationHub
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Ensembl release 80 is out!

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