User: Julie Zhu

gravatar for Julie Zhu
Julie Zhu3.8k
Reputation:
3,830
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Trusted
Location:
United States
Website:
https://profiles.umass...
Last seen:
3 weeks, 4 days ago
Joined:
9 years, 3 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 • 525 results • page 1 of 53 • next >
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Comment: C: CRISPRseek scoring clarification
... Hi Dawid, Could you please let me know your session info? If possible, could you please post your code and an example input file? Thanks! Best regards, Julie ...
written 4 weeks ago by Julie Zhu3.8k
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Answer: A: Problem installing CRISPRseek
... Please try to install the CRISPRseek using source("http://bioconductor.org/biocLite.R") biocLite("CRISPRseek") Best regards, Julie On Oct 8, 2018, at 8:47 AM, ldumas9 [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post you are following on su ...
written 5 weeks ago by Julie Zhu3.8k
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Comment: C: ATACseqQC memory overflow issue
... Thanks to Jianhong, the memory issue has be fixed in the development version. Here are the scripts to install the dev version of ATACseqQC. library(devtools); install_github("jianhong/ATACseqQC") Please set bigFile=TRUE when using readBamFile. Thanks! Best regards, Julie ...
written 5 weeks ago by Julie Zhu3.8k
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Comment: C: ATACseqQC memory overflow issue
... One of the developers, Jianhong, will work on making it work with big bam files. For now, please try to generate the plots using a couple of chromosomes from your BAM files. Thanks! Best regards, Julie ...
written 5 weeks ago by Julie Zhu3.8k
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Comment: C: ChIPpeakAnno overlap peaks with TSS returns more than TSS overlap
... Could you please try the following code and see if that meets your need? Thanks! tss <- promoters(TxDb.Mmusculus.UCSC.mm10.knownGene, upstream=0, downstream=1) ChIP_peaks_annoTSS <- annotatePeakInBatch(res1_ChIP,                                             AnnotationData = tss,               ...
written 7 weeks ago by Julie Zhu3.8k
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Comment: C: the closest gene to a breakpoint
... Bogdan, The function annoPeaks works as well. Best, Julie Activity ...
written 11 weeks ago by Julie Zhu3.8k
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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 11 weeks ago by Julie Zhu3.8k
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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 3 months ago by Julie Zhu3.8k
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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 4 months ago by Julie Zhu3.8k
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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 4 months ago by Julie Zhu3.8k

Latest awards to Julie Zhu

Popular Question 7 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 16 months ago, created an answer that has been accepted. For A: GUIDESeq analysis - handling biological and technical replicates
Scholar 16 months ago, created an answer that has been accepted. For A: offTargetAnalysis() Error in weights %*% mismatch.pos : non-conformable argument
Scholar 16 months ago, created an answer that has been accepted. For A: DistanceToNearest Not giving nearest Range
Teacher 16 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 16 months ago, created an answer that has been accepted. For A: How to find nearest CpG islands around miRNA genes using granges?
Scholar 16 months ago, created an answer that has been accepted. For A: createBarcodeFasta in GUIDEseq
Popular Question 16 months ago, created a question with more than 1,000 views. For CRISPRseek question on scoring
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
Scholar 16 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 20 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 3.9 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 4.2 years ago, created 100 posts.

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