User: Julie Zhu

gravatar for Julie Zhu
Julie Zhu3.9k
Reputation:
3,850
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Trusted
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United States
Website:
https://profiles.umass...
Last seen:
17 hours ago
Joined:
9 years, 4 months ago
Email:
j********@umassmed.edu

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 • 530 results • page 2 of 53 • next >
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Comment: C: the closest gene to a breakpoint
... Bogdan, The function annoPeaks works as well. Best, Julie Activity ...
written 3 months ago by Julie Zhu3.9k
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Answer: A: the closest gene to a breakpoint
... Bogdan, AnnotatePeakInBatch in the ChIPpeakAnno package should do. https://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html Best regards, Julie ...
written 3 months ago by Julie Zhu3.9k
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Answer: A: CRISPRseek: offTargetAnalysis -> buildFeatureVectorForScoring increase max.misma
... Jacob, The following parameters need to be reset. BSgenomeName = Mmusculus, chromToSearch = "all" Best regards, Julie On Jul 29, 2018, at 7:37 PM, jacob.bradford [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on supp ...
written 4 months ago by Julie Zhu3.9k
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Comment: C: use factorFootprints function in ATACseqQC to get DNA footprinting for certain g
... Aimin, I suggest not set bindingSites unless you really know where the binding sites are. Best, Julie ...
written 5 months ago by Julie Zhu3.9k
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Comment: C: use factorFootprints function in ATACseqQC to get DNA footprinting for certain g
... Aimin,   Please use my following example,    which <- GRanges(seqnames = "chr1", ranges = IRanges(seq(10000, 2000000, by=1000), width = 100), score = rep(1,1991)) seqlengths(which)[1] = 248956422 Best,   Julie ...
written 5 months ago by Julie Zhu3.9k
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Answer: A: use factorFootprints function in ATACseqQC to get DNA footprinting for certain g
... Aimin, Score is required here. The following example should run fine. which <- GRanges(seqnames = "chr1", ranges = IRanges(seq(10000, 2000000, by=1000), width = 100), score = rep(1,1991)) seqlengths(which)[1] = 248956422 bamfile <- system.file("extdata", "GL1.bam",                         ...
written 5 months ago by Julie Zhu3.9k
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Comment: C: use factorFootprints function in ATACseqQC to get DNA footprinting for certain g
... Aimin, The bindingSites you set might not contain any CTCF binding sites. Please try to run the analysis without setting the parameter bindingSites. By default, the program will perform genome-wide search of the CTCF binding sites.  Best, Julie ...
written 5 months ago by Julie Zhu3.9k
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Answer: A: ATACseqQC: a few questions
... David, Thanks for the feedback! Regarding the output from cumulativePercentage, you are unlikely to get a plot that looks exactly the same as the one shown in the vignette. The further away from the y = x line the curve is, the higher the signal noise ratio is. We will add the Transcription Start ...
written 5 months ago by Julie Zhu3.9k
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Answer: A: A unexpected error occurred when using CRISPRseek package
... Ming-Ru, Thanks for the detailed description of the problem and the session information! What happened is that the mutated gRNA does not have a perfect matched target site on chromosome X. The error occurred because you were trying to search for RE sites on the flanking regions of a non-extent gen ...
written 5 months ago by Julie Zhu3.9k
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Answer: A: How to understand Summary.xls in output of CRISPRseek
... Jianhong, Your understanding of all the columns is correct except uniqueREin200, which contains the unique restriction enzyme names in upstream 100 and downstream 100 around the gRNA. Best, Julie ...
written 6 months ago by Julie Zhu3.9k

Latest awards to Julie Zhu

Popular Question 11 weeks 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 6 months ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Popular Question 6 months ago, created a question with more than 1,000 views. For GEOquery
Scholar 17 months ago, created an answer that has been accepted. For A: GUIDESeq analysis - handling biological and technical replicates
Scholar 17 months ago, created an answer that has been accepted. For A: offTargetAnalysis() Error in weights %*% mismatch.pos : non-conformable argument
Scholar 17 months ago, created an answer that has been accepted. For A: DistanceToNearest Not giving nearest Range
Teacher 17 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 17 months ago, created an answer that has been accepted. For A: How to find nearest CpG islands around miRNA genes using granges?
Scholar 17 months ago, created an answer that has been accepted. For A: createBarcodeFasta in GUIDEseq
Popular Question 17 months ago, created a question with more than 1,000 views. For CRISPRseek question on scoring
Popular Question 17 months ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Popular Question 17 months ago, created a question with more than 1,000 views. For GEOquery
Scholar 17 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 21 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 4.0 years ago, created an answer that has been accepted. For A: ChIPpeakAnno: Non-empty IRange object in case of no overlap
Autobiographer 4.2 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 4.3 years ago, created 100 posts.

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