User: Julie Zhu

gravatar for Julie Zhu
Julie Zhu4.1k
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Website:
https://profiles.umass...
Last seen:
2 days, 2 hours ago
Joined:
10 years, 3 months 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 • 605 results • page 1 of 61 • next >
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Comment: C: CRISPR SEEK TxDb issue
... Hi Xin, Great to hear that! Thanks for letting me know! Best wishes, Julie ...
written 2 days ago by Julie Zhu4.1k
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Comment: C: CRISPRseek ERROR, can't read featureWeightMatrix in, wrong data format
... Hi Nils, Thanks for your effort and for letting me know your solution! Best, Julie ...
written 2 days ago by Julie Zhu4.1k
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Answer: A: CRISPR SEEK TxDb issue
... Hi Xin, Please follow the script from Hervé or James to create the txdb for the pig genome, then set the parameter txdb and orgAnn in the offtargetAnalysis function call, e.g., txdb = txdb.susScr11.UCSC, orgAnn = org.Ss.egSYMBOL after you run the following script. About the warning message, it shou ...
written 2 days ago by Julie Zhu4.1k
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Comment: C: CRISPRseek ERROR, can't read featureWeightMatrix in, wrong data format
... Nils, I am sorry to let you know that it is possible that the new Bioconductor release no longer supports geneRfold installation in window. Best regards, Julie ...
written 3 days ago by Julie Zhu4.1k
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Comment: C: CRISPRseek ERROR, can't read featureWeightMatrix in, wrong data format
... Hi Nils, If you would like to fold the gRNAs, you could try this. Step 1. install most recent version of Viennerna package Step 2. install geneR in bioconductor (first download the source code, then use install.package in R to install it, e.g., geneR2.22.0.tar.gz) Step 3. install GeneRfold (downlo ...
written 9 days ago by Julie Zhu4.1k
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Comment: C: CRISPRseek ERROR, can't read featureWeightMatrix in, wrong data format
... Hi Nils, Unfortunately, geneRfold has been deprecated. Please let me know if you really need to fold the gRNAs, and I will share a workaround. BTW, please set subPAM.activity for Cpf1. For example, set TT = 1, GG = 0, CC =0, AA =0, AC =0. Best regards, Julie ...
written 10 days ago by Julie Zhu4.1k
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Comment: C: CRISPRseek ERROR, can't read featureWeightMatrix in, wrong data format
... Hi Nils, Great to know that you have successfully obtained the efficacy prediction score. Yes, the warning Message about search2hits means that there is no offtarget found for your searching criteria. You could try to set allowed.mismatch.PAM = 2 and PAM.pattern = "^TNNN" if you would like to find ...
written 11 days ago by Julie Zhu4.1k
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Answer: A: CRISPRseek ERROR, can't read featureWeightMatrix in, wrong data format
... Nils, Please try to set baseBeforegRNA = 8, baseAfterPAM = 23 for Cpf1. If your input sequence is not expected to be present in the genome, please set useEfficacyFromInputSeq = TRUE. In addition, the function expects featureWeightMatrix to be a file path. To use DoenchNBT2014.csv included in the pa ...
written 15 days ago by Julie Zhu4.1k
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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 10 weeks ago by Julie Zhu4.1k
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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 10 weeks ago by Julie Zhu4.1k

Latest awards to Julie Zhu

Popular Question 10 months ago, created a question with more than 1,000 views. For CRISPRseek question on scoring
Popular Question 10 months ago, created a question with more than 1,000 views. For GEOquery
Popular Question 10 months ago, created a question with more than 1,000 views. For CRISPRseek question on scoring
Scholar 10 months ago, created an answer that has been accepted. For A: createBarcodeFasta in GUIDEseq
Popular Question 10 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 org.Sc.sgd.db: Yeast ensembl ID to entrez ID conversion problem
Popular Question 18 months ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Popular Question 18 months ago, created a question with more than 1,000 views. For GEOquery
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Popular Question 2.4 years ago, created a question with more than 1,000 views. For GEOquery
Popular Question 2.4 years ago, created a question with more than 1,000 views. For CRISPRseek question on scoring
Teacher 2.4 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 2.4 years ago, created an answer that has been accepted. For A: How to find nearest CpG islands around miRNA genes using granges?
Scholar 2.4 years ago, created an answer that has been accepted. For A: GUIDESeq analysis - handling biological and technical replicates
Scholar 2.4 years ago, created an answer that has been accepted. For A: offTargetAnalysis() Error in weights %*% mismatch.pos : non-conformable argument
Scholar 2.4 years ago, created an answer that has been accepted. For A: DistanceToNearest Not giving nearest Range
Scholar 2.4 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 2.4 years ago, created an answer that has been accepted. For A: createBarcodeFasta in GUIDEseq
Popular Question 2.7 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 4.9 years ago, created an answer that has been accepted. For A: ChIPpeakAnno: Non-empty IRange object in case of no overlap
Autobiographer 5.2 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 5.2 years ago, created 100 posts.

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