User: Julie Zhu

gravatar for Julie Zhu
Julie Zhu3.8k
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Last seen:
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Joined:
8 years, 7 months ago
Email:
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Lihua Julie Zhu, Ph.D

Research Professor

Department of Molecular, Cell and Cancer Biology (MCCB)

Head of MCCB Bioinformatics Core

Program in Bioinformatics and Integrative Biology

Program in Molecular Medicine

University of Massachusetts Medical School

364 Plantation Street, Room 613

Worcester, MA 01605

508-856-5256 phone

(508) 856 5460 fax

https://profiles.umassmed.edu/display/129880

Posts by Julie Zhu

<prev • 507 results • page 1 of 51 • next >
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Answer: A: integer overflow in ChIPpeakAnno assignChromosomeRegion
... Janet, Thanks for the feedback! The Jaccard index, also known as Intersection over Union. The Jaccard index is between 0 and 1. The higher the index, the more significant the overlap between the peak region and the genomic features in consideration. Best regards, Julie On Feb 14, 2018, at 5:07 ...
written 5 days ago by Julie Zhu3.8k
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Answer: A: ATACseqQC memory overflow issue
... José, Thanks for the feedback! Jianhong, one of the developers will work with you on the coding side. For now, please try to generate the plots using a couple of chromosomes from your BAM files. FYI, we have tested the effects of sequencing depth on the patterns in various diagnostic plots using ...
written 8 days ago by Julie Zhu3.8k
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Comment: C: CRISPRseek offTargetAnalysis errors
... Joyce, Could you please send me the input data that causes this error? Thanks! Best regards, Julie From: "joyce [bioc]" <noreply@bioconductor.org> Reply-To: "reply+02b21e37+code@bioconductor.org" <reply+02b21e37+code@bioconductor.org> Date: Sunday, January 14, 2018 at 7:08 PM To: "Z ...
written 5 weeks ago by Julie Zhu3.8k
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Comment: C: CRISPRseek offTargetAnalysis errors
... Joyce, I tested the two sequences and both worked for me. library(CRISPRseek) library("BSgenome.Mmusculus.UCSC.mm10") FYI, I used CRISPRseek_1.18.0 and Biostrings_2.46.0. Please make sure that you have the right version of the packages installed. offTargetAnalysis(DNAStringSet("ATGGCTTCACAGCTGCC ...
written 5 weeks ago by Julie Zhu3.8k
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Answer: A: CRISPRseek offTargetAnalysis error
... Joyce, The post at an erro related with RNAStringSet seems to suggest that there are non-DNA characters in your input sequences. Could you please post a couple of sequences for me to reproduce the error you encountered? Thanks! Best regards, Julie From: "joyce [bioc]" <noreply@bioconducto ...
written 5 weeks ago by Julie Zhu3.8k
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Answer: A: CRISPRseek offTargetAnalysis error
... Joyce, It seems to be related to the UCSC BSgenome package you installed. You might want to update it. This post might be helpful to you. problems in installing BSgenome.Mmusculus.UCSC.mm10 Best, Julie Activity on a post you are following on support.bioconductor.org<https: support.biocondu ...
written 9 weeks ago by Julie Zhu3.8k
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Comment: C: DistanceToNearest Not giving nearest Range
... You are very welcome! Best regards, Julie Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User chitsazanalex<https: support.bioconductor.org="" u="" 11765=""/> wrote Comment: DistanceToNearest Not giving nearest Range<https: sup ...
written 9 weeks ago by Julie Zhu3.8k
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Answer: A: DistanceToNearest Not giving nearest Range
... Ok. If you set ignore.strand = TRUE, you will get the one with shortest distance. distanceToNearest(x, TSS, ignore.strand= TRUE) Hits object with 1 hit and 1 metadata column:       queryHits subjectHits |  distance       <integer>   <integer> | <integer>   [1]         1            ...
written 10 weeks ago by Julie Zhu3.8k
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Answer: A: DistanceToNearest Not giving nearest Range
... Looks like that you are trying to annotate peaks. If that is the case, you might want to try the function annotatePeakInBatch in the ChIPpeakAnno package http://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html. Best regards, Julie Activity on a post you are following on support.bioco ...
written 10 weeks ago by Julie Zhu3.8k
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Answer: A: ATACseqQC needs too much memory
... Michael, The most recent version of ATACseqQC at http://bioconductor.org/packages/devel/bioc/html/ATACseqQC.html should run faster. Best regards, Julie ...
written 10 weeks ago by Julie Zhu3.8k

Latest awards to Julie Zhu

Popular Question 11 months ago, created a question with more than 1,000 views. For build TSS from biomaRt for ChIPpeakAnno, how to decide the mm9 and mm10 assembly?
Scholar 3.2 years ago, created an answer that has been accepted. For A: ChIPpeakAnno: Non-empty IRange object in case of no overlap
Autobiographer 3.4 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 3.4 years ago, created 100 posts.

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