User: Julie Zhu

gravatar for Julie Zhu
Julie Zhu4.0k
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United States
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https://profiles.umass...
Last seen:
1 week, 5 days ago
Joined:
10 years, 1 month ago
Email:
j********@umassmed.edu

Lihua Julie Zhu, Ph.D

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 • 597 results • page 1 of 60 • next >
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Answer: A: Help with using CRISPRseeker
... Sharvari, I have added a new parameter ignore.strand in the offtargetAnalysis function (default to TRUE). To obtain strand-specific gene annotation, set ignore.strand = FALSE. You can download Version: 1.25.7 using the following command. git clone https://git.bioconductor.org/packages/CRISPRseek T ...
written 14 days ago by Julie Zhu4.0k
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Comment: C: Help with using CRISPRseeker
... Sharvari, This is intended since gRNA efficacy is only applicable to the on-target. Best regards, Julie ...
written 16 days ago by Julie Zhu4.0k
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Answer: A: Help with using CRISPRseeker
... Sharvari, You can either wait for a couple of days for version 1.25.5 to propagate to http://bioconductor.org/packages/devel/bioc/html/CRISPRseek.html, or get the source code using git clone. git clone https://git.bioconductor.org/packages/CRISPRseek Best, Julie ...
written 19 days ago by Julie Zhu4.0k
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Comment: C: Help with using CRISPRseeker
... Hi Sharvari, Please download the Version: 1.25.5 of CRISPRseek package to run your script using rule set 2 and max.mismatches > 3. Please let me know if it does not work for you. Best, Julie ...
written 20 days ago by Julie Zhu4.0k
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Answer: A: Help with using CRISPRseeker
... Hi Sharvari, Please download Version: 1.25.4 for strand-specific annotation at http://bioconductor.org/packages/devel/bioc/html/CRISPRseek.html. It might take a couple of days for it to propagate. Alternatively, you could download the most recent version using git git clone git@git.bioconductor.org ...
written 20 days ago by Julie Zhu4.0k
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Answer: A: Help with using CRISPRseeker
... Hi Sharvari, Just to let you know that you can set max.mismatch = 0 to speed up the analysis if you are only interested in obtaining the gRNA efficacy. The higher number you set max.mismatch, the slower the analysis takes. Best regards, Julie ...
written 21 days ago by Julie Zhu4.0k
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Comment: C: Help with using CRISPRseeker
... Sharvari, I am glad that you got it to work using python 2.7. Could you please try to run the following script (rule set 1) with max.mismatch = 3 to see if the error goes away? results <- offTargetAnalysis(inputFilePath = gRNAFilePath, findgRNAsWit ...
written 21 days ago by Julie Zhu4.0k
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Answer: A: GUIDEseq Error in GAlignmentPairs
... Tomás, I am able to run the analysis with your data without any issue. Here is my sessionInfo and the test script. I would be happy to test your script if you could share it with me. Best regards, Julie library("BSgenome.Hsapiens.UCSC.hg38") library("org.Hs.eg.db") library(("TxDb.Hsapiens.UCSC.hg38 ...
written 21 days ago by Julie Zhu4.0k
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Comment: C: Help with using CRISPRseeker
... Sharvari, Please try the following script. results <- offTargetAnalysis(inputFilePath = gRNAFilePath, findgRNAsWithREcutOnly = FALSE, REpatternFile = REpatternFile, scoring.method = "CFDscore", findPairedgRNAOnly = FA ...
written 21 days ago by Julie Zhu4.0k
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Answer: A: Help with using CRISPRseeker
... Hi Sharvari, It is the same as used in the manual. Best regards, Julie ...
written 21 days ago by Julie Zhu4.0k

Latest awards to Julie Zhu

Popular Question 8 months ago, created a question with more than 1,000 views. For CRISPRseek question on scoring
Popular Question 8 months ago, created a question with more than 1,000 views. For GEOquery
Popular Question 8 months ago, created a question with more than 1,000 views. For CRISPRseek question on scoring
Scholar 8 months ago, created an answer that has been accepted. For A: createBarcodeFasta in GUIDEseq
Popular Question 8 months ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Popular Question 12 months ago, created a question with more than 1,000 views. For org.Sc.sgd.db: Yeast ensembl ID to entrez ID conversion problem
Popular Question 16 months ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Popular Question 16 months ago, created a question with more than 1,000 views. For GEOquery
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Popular Question 2.2 years ago, created a question with more than 1,000 views. For GEOquery
Popular Question 2.2 years ago, created a question with more than 1,000 views. For CRISPRseek question on scoring
Teacher 2.2 years 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 2.2 years ago, created an answer that has been accepted. For A: How to find nearest CpG islands around miRNA genes using granges?
Scholar 2.2 years ago, created an answer that has been accepted. For A: GUIDESeq analysis - handling biological and technical replicates
Scholar 2.2 years ago, created an answer that has been accepted. For A: offTargetAnalysis() Error in weights %*% mismatch.pos : non-conformable argument
Scholar 2.2 years ago, created an answer that has been accepted. For A: DistanceToNearest Not giving nearest Range
Scholar 2.2 years ago, created an answer that has been accepted. For A: What are out-of-bound ranges? Is it necessary to get rid of them?
Scholar 2.2 years ago, created an answer that has been accepted. For A: createBarcodeFasta in GUIDEseq
Popular Question 2.5 years 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 4.8 years ago, created an answer that has been accepted. For A: ChIPpeakAnno: Non-empty IRange object in case of no overlap
Autobiographer 5.0 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 5.0 years ago, created 100 posts.

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