User: Julie Zhu

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Julie Zhu3.8k
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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 • 495 results • page 1 of 50 • next >
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Analyzing CIRCLE-seq data using GUIDEseq package
... Keith, GUIDEseq package can be used to analyze CIRCLE-seq too. During the preprocessing steps, you will not need to remove adaptors introduced in the GUIDE-seq protocol. In addition, you will need to set the max.R1.len =150 and max.R2.len = 150 using the GUIDEseqAnalysis function in GUIDEseq packag ...
guideseq circle-seq written 20 days ago by Julie Zhu3.8k
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Answer: A: CRISPRseek gRNA efficacy
... Joyce, Here is a description of the parameter useEfficacyFromInputSeq. Default FALSE. If set to TRUE, summary file will contain gRNA efficacy calculated from input sequences instead of from off-target analysis. Set it to TRUE if the input sequence is from a different species than the one used for o ...
written 22 days ago by Julie Zhu3.8k
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Comment: C: CRISPRseek CFD score
... Joyce, Glad to help! Great that you found the cause of problem. Thanks for letting me know! Best regards, Julie ...
written 26 days ago by Julie Zhu3.8k
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Comment: C: CRISPRseek CFD score
... Joyce, I tried offtarget analysis with your test sequence and human genome. I  was able to generate the InExon information. Here is the code snippet. Best regards, Julie    library(CRISPRseek)     library("BSgenome.Hsapiens.UCSC.hg19")     library(TxDb.Hsapiens.UCSC.hg19.knownGene)     librar ...
written 27 days ago by Julie Zhu3.8k
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Answer: A: Does CRISPRSEEK work on previously unknown genomes?
... Yanmei, Thanks for taking time to post the question! https://bioconductor.org/packages/3.5/BiocViews.html#___BSgenome lists BSgenomes that can be directly used as input to CRISPRseek . For detailed information on how to use the package, please read the user guide at http://bioconductor.org/package ...
written 28 days ago by Julie Zhu3.8k
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Comment: C: CRISPRseek CFD score
... Joyce, Please post the code for setting ss and txdb. What you posted is the amazon objects which I do not have access to. Thanks! Best regards, Julie ...
written 29 days ago by Julie Zhu3.8k
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Answer: A: CRISPRseek CFD score
... Joyce, Thanks for the great question! Different applications place different emphasis on efficacy vs offTarget score. For example, in vitro screening assays are more interested in efficacy score, while therapeutic studies cannot tolerate even small offTarget effects. Therefore, it is very hard to c ...
written 4 weeks ago by Julie Zhu3.8k
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Comment: C: CRISPRseek scoring clarification
... Dawid, Glad that it works for you. If you set annotateExon = TRUE, txdb and orgAnn, then you should get the annotation information. I removed them for speeding up the test. BTW, I added your example as one of the integration tests in CRISPRseek. Hope it is all right with you. FYI, I changed the ...
written 4 weeks ago by Julie Zhu3.8k
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Answer: A: could not find function "hash"
... Joyce, Please trying the following command. library("hash") results=offTargetAnalysis("exon.fasta", findgRNAsWithREcutOnly = FALSE, annotateExon = TRUE, annotatePaired = FALSE, findPairedgRNAOnly = FALSE, txdb= txdb, max.mismatch = 3, BSgenomeName = ss, outputDir = ".", overwrite = TRUE,scoring.me ...
written 4 weeks ago by Julie Zhu3.8k
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Comment: C: CRISPRseek scoring clarification
... Dawid, Please try to use the following command to download the most recent version. git clone git@git.bioconductor.org:packages/CRISPRseek Best regards, Julie From: "Dawid G. Nowak [bioc]" <noreply@bioconductor.org> Reply-To: "reply+0df74aaa+code@bioconductor.org" <reply+0df74aaa+code@b ...
written 4 weeks ago by Julie Zhu3.8k

Latest awards to Julie Zhu

Popular Question 8 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 2.9 years ago, created an answer that has been accepted. For A: ChIPpeakAnno: Non-empty IRange object in case of no overlap
Autobiographer 3.2 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 3.2 years ago, created 100 posts.

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