User: Julie Zhu

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Julie Zhu3.8k
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https://profiles.umass...
Last seen:
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Joined:
9 years, 1 month ago
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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 • 520 results • page 2 of 52 • next >
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Answer: A: CFDscore calculations used in CRISPRseek
... Dawid, 1. Yes, “CFDscore” in CRISPRseek is calculated based on the table “NatureBiot2016SuppTable19DoenchRoot" (Doench et al., 2016) and Percent-Active column. 2. CFDscore is calculated using mismatch type and mismatch position although the mismatch activity is given as pos 20, 19, 18,....1 ...
written 3 months ago by Julie Zhu3.8k
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Job: Senior Bioinformatician position at University of Massachusetts Medical School, Worcester, MA
... Hi, We have a senior Bioinformatician/Computational Biologist position available at University of Massachusetts Medical School.  Please see the job description below. To apply online, please go to    https://www.ummsjobs.com/job/3124/ Thanks for your attention!   Kind regards,   Julie   OV ...
job see senior bioinformatician position written 5 months ago by Julie Zhu3.8k
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Answer: A: motif enrichment analysis for protein sequences
... Please take a look at https://www.bioconductor.org/packages/release/bioc/html/dagLogo.html and see if dagLogo fits your needs. Thanks! Best regards, Julie On Mar 6, 2018, at 9:58 PM, petyuk [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post y ...
written 6 months ago by Julie Zhu3.8k
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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 7 months 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 7 months 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 8 months 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 8 months 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 8 months 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 months 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 months ago by Julie Zhu3.8k

Latest awards to Julie Zhu

Popular Question 4 months ago, created a question with more than 1,000 views. For GEOquery
Popular Question 4 months ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Scholar 14 months ago, created an answer that has been accepted. For A: DistanceToNearest Not giving nearest Range
Scholar 14 months ago, created an answer that has been accepted. For A: createBarcodeFasta in GUIDEseq
Popular Question 14 months ago, created a question with more than 1,000 views. For CRISPRseek question on scoring
Popular Question 14 months ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Popular Question 14 months ago, created a question with more than 1,000 views. For GEOquery
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: What are out-of-bound ranges? Is it necessary to get rid of them?
Scholar 14 months ago, created an answer that has been accepted. For A: How to find nearest CpG islands around miRNA genes using granges?
Scholar 14 months ago, created an answer that has been accepted. For A: GUIDESeq analysis - handling biological and technical replicates
Scholar 14 months ago, created an answer that has been accepted. For A: offTargetAnalysis() Error in weights %*% mismatch.pos : non-conformable argument
Scholar 14 months ago, created an answer that has been accepted. For A: What are out-of-bound ranges? Is it necessary to get rid of them?
Popular Question 18 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 3.8 years ago, created an answer that has been accepted. For A: ChIPpeakAnno: Non-empty IRange object in case of no overlap
Autobiographer 4.0 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 4.0 years ago, created 100 posts.

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