User: Julie Zhu

gravatar for Julie Zhu
Julie Zhu4.0k
Reputation:
4,010
Status:
Trusted
Location:
United States
Website:
https://profiles.umass...
Last seen:
9 hours ago
Joined:
9 years, 11 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 • 578 results • page 1 of 58 • next >
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Answer: A: ATAC-QC shiftGAlignmentsList function
... Shuang, I just noticed that you have a typo in the following code. bamTop100 <- scanBam(BamFile(bamfilde, yieldSize = 100), param = ScanBamParam(tag=possibleTag))[[1]]$tag It should be bamfile instead of bamfilde. bamTop100 <- scanBam(BamFile(bamfile, yieldSize ...
written 9 hours ago by Julie Zhu4.0k
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Comment: C: ATACseqQC splitGAlignmentsByCut: strand values must be in '+' '-' '*'
... Thanks! The main developer Jianhong will work on it and post the solutions here. Best regards, Julie ...
written 1 day ago by Julie Zhu4.0k
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Answer: A: ATACseqQC splitGAlignmentsByCut: strand values must be in '+' '-' '*'
... Could you please share your session information with us? The most recent release of ATACseqQC is 1.8.1 (https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html). Thanks! Best regards, Julie ...
written 1 day ago by Julie Zhu4.0k
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Answer: A: ATAC-QC shiftGAlignmentsList function
... Thanks Jim for identifying the issue! Shuang, could you please use the most recent release ATACseqQC 1.8.1 (Bioc 3.9 and R 3.6) at https://bioconductor.org/packages/release/bioc/html/ATACseqQC.html? Thanks! Best regards, Julie ...
written 1 day ago by Julie Zhu4.0k
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Answer: A: ATAC-QC fragSizeDist function
... Shuang, It seem that your library contains a lot of mitochondria DNA, which is a waste of reads. For your future reference, it is more efficient to deplete mitochondria DNA when constructing the ATAC-seq sequencing library. I am wondering what the fragment size distribution looks like (ATACseqQC::fr ...
written 1 day ago by Julie Zhu4.0k
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Job: Senior Bioinformatician - University of Massachusetts Medical School
... OVERVIEW: In MCCB of University of Massachusetts Medical School, we have developed a core team of accomplished computational biologists who work side-by-side with bench scientists to evaluate, select and develop algorithms and software pipelines to analyze, annotate, visualize and integrate various ...
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Job: A post-doctoral position in bioinformatics and computational biology at Umass Medical School
... A post-doctoral position in bioinformatics and computational biology is available in Prof. Julie Zhu's group in the Department of Molecular, Cell and Cancer Biology at the University of Massachusetts Medical School, located in Worcester MA. Research projects in Dr. Zhu's group include (1) developme ...
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Answer: A: CRISPRseek:::findgRNAs paired gRNAs with PAM inward orientation
... Saba, Please download the newest version of CRISPRseek (Version: 1.25.2). To find paired gRNAs with PAM face inwards towards each other, please set paired.orientation = "PAMin". To obtain the most recent dev version of CRISPRseek, please type the following command in a terminal. git clone git@git ...
written 28 days ago by Julie Zhu4.0k
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Answer: A: CRISPRseek:::findgRNAs paired gRNAs with PAM inward orientation
... Saba, Thanks for posting the question! I will add the functionality and let you know when it is done. Best regards, Julie ...
written 28 days ago by Julie Zhu4.0k
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Comment: C: Genomic Coordinate Annoation
... You are very welcome! Please note that I changed "both" to "overlapping" in the above post to fit your needs. Best regards, Julie ...
written 10 weeks 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 CRISPRseek question on scoring
Popular Question 6 months ago, created a question with more than 1,000 views. For GEOquery
Popular Question 6 months ago, created a question with more than 1,000 views. For CRISPRseek question on scoring
Scholar 6 months ago, created an answer that has been accepted. For A: createBarcodeFasta in GUIDEseq
Popular Question 6 months ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Popular Question 9 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 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
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Popular Question 2.1 years ago, created a question with more than 1,000 views. For GEOquery
Popular Question 2.1 years ago, created a question with more than 1,000 views. For CRISPRseek question on scoring
Teacher 2.1 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 2.1 years ago, created an answer that has been accepted. For A: How to find nearest CpG islands around miRNA genes using granges?
Scholar 2.1 years ago, created an answer that has been accepted. For A: GUIDESeq analysis - handling biological and technical replicates
Scholar 2.1 years ago, created an answer that has been accepted. For A: offTargetAnalysis() Error in weights %*% mismatch.pos : non-conformable argument
Scholar 2.1 years ago, created an answer that has been accepted. For A: DistanceToNearest Not giving nearest Range
Scholar 2.1 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 2.1 years ago, created an answer that has been accepted. For A: createBarcodeFasta in GUIDEseq
Popular Question 2.3 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 4.6 years ago, created an answer that has been accepted. For A: ChIPpeakAnno: Non-empty IRange object in case of no overlap
Autobiographer 4.8 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 4.8 years ago, created 100 posts.

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