User: Julie Zhu

gravatar for Julie Zhu
Julie Zhu4.0k
Reputation:
3,990
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Trusted
Location:
United States
Website:
https://profiles.umass...
Last seen:
1 week ago
Joined:
9 years, 7 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 • 566 results • page 1 of 57 • next >
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Comment: C: CRISPRseek scoring clarification
... Nan, Thanks for posting the code and gRNAs! FYI, CFD score of 1 means perfect match. Is it corret that the following two are the on-targets instead of off-targets? Do you find any off-targets for these two gRNAs? Thanks! I just ran your testing code and there is no offtarget found for either of ...
written 7 days ago by Julie Zhu4.0k
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Comment: C: CRISPRseek scoring clarification
... Nan, A great question! Could you please look at one of the output files offTargets.xls to compare the two gRNAs and their offTargets to see if there are any differences in terms of their offTargets? If it is still hard to distinguish these two cases, could you please post the two gRNA sequences an ...
written 7 days ago by Julie Zhu4.0k
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Comment: C: My post or response to post does not get sent to the Bioconductor email list
... Thanks so much, Lori! FYI, I posted the issue at github a couple of weeks ago. Best regards, Julie ...
written 14 days ago by Julie Zhu4.0k
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Comment: C: Unable to generate feature vector with custom genome in cleanUpdTSeq
... Danielle, You will need to remove anything after | and any spaces before that. For example, use GLCHR01 to replace “ GLCHR01 | organism=GiardiaAssemblageAisolateWB | version=2013-02-08 | length=1491578 | SO=chromosome =2013-02-08 | length=863 | SO=supercontig” Best, Julie ...
written 15 days ago by Julie Zhu4.0k
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Comment: C: Unable to generate feature vector with custom genome in cleanUpdTSeq
... Danielle, I believe your guess is correct, i.e., it reads the chromosome names directly from the fasta file provided. There are probably issues with the fasta file itself. You can open the fasta file to see what is the first line. Alternatively, you can use grep to find all the chromosome names in ...
written 15 days ago by Julie Zhu4.0k
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My post or response to post does not get sent to the Bioconductor email list
... Hi, I am still have problem with my posts or response to others' post, i.e., my posts are not being sent out to the Bioconductor email list. Could you please help? Thanks! Best regards, Julie ...
posts email written 15 days ago by Julie Zhu4.0k
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Comment: C: Unable to generate feature vector with custom genome in cleanUpdTSeq
... Danielle, If you look at the seqnames column, you will see that your peak ranges are located in different chromosomes such as GLCHR03 and GL50803. In order to obtain sequence from these different chromosomes, the BSgenome needs to have the matched chromosome name. Dose it make sense? Thanks! Be ...
written 15 days ago by Julie Zhu4.0k
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Answer: A: Unable to generate feature vector with custom genome in cleanUpdTSeq
... Danielle, Could you please type the following and post the output? I would like to see the chromosome names in the peaks_grange. Thanks! peaks_grange Best regards, Julie ...
written 15 days ago by Julie Zhu4.0k
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Answer: A: Unable to generate feature vector with custom genome in cleanUpdTSeq
... Danielle, Could you please type the following and post the output? I would like to see the chromosome names in the peaks_grange. Thanks! peaks_grange Best regards, Julie ...
written 15 days ago by Julie Zhu4.0k
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Comment: C: CRISPRseek scoring clarification
... You are welcome, Nan! Yes, CFD score is the same! Best regards, Julie ...
written 17 days ago by Julie Zhu4.0k

Latest awards to Julie Zhu

Popular Question 6 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 10 months ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Popular Question 10 months ago, created a question with more than 1,000 views. For GEOquery
Scholar 21 months ago, created an answer that has been accepted. For A: GUIDESeq analysis - handling biological and technical replicates
Scholar 21 months ago, created an answer that has been accepted. For A: offTargetAnalysis() Error in weights %*% mismatch.pos : non-conformable argument
Scholar 21 months ago, created an answer that has been accepted. For A: DistanceToNearest Not giving nearest Range
Teacher 21 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 21 months ago, created an answer that has been accepted. For A: How to find nearest CpG islands around miRNA genes using granges?
Scholar 21 months ago, created an answer that has been accepted. For A: createBarcodeFasta in GUIDEseq
Popular Question 21 months ago, created a question with more than 1,000 views. For CRISPRseek question on scoring
Popular Question 21 months ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Popular Question 21 months ago, created a question with more than 1,000 views. For GEOquery
Scholar 21 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 2.0 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 4.3 years ago, created an answer that has been accepted. For A: ChIPpeakAnno: Non-empty IRange object in case of no overlap
Autobiographer 4.5 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 4.5 years ago, created 100 posts.

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