User: Julie Zhu

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Julie Zhu3.8k
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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 • 511 results • page 2 of 52 • next >
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Comment: C: DistanceToNearest Not giving nearest Range
... You are very welcome! Best regards, Julie Activity on a post you are following on support.bioconductor.org<https: support.bioconductor.org=""> User chitsazanalex<https: support.bioconductor.org="" u="" 11765=""/> wrote Comment: DistanceToNearest Not giving nearest Range<https: sup ...
written 6 months ago by Julie Zhu3.8k
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Answer: A: DistanceToNearest Not giving nearest Range
... Ok. If you set ignore.strand = TRUE, you will get the one with shortest distance. distanceToNearest(x, TSS, ignore.strand= TRUE) Hits object with 1 hit and 1 metadata column:       queryHits subjectHits |  distance       <integer>   <integer> | <integer>   [1]         1            ...
written 6 months ago by Julie Zhu3.8k
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Answer: A: DistanceToNearest Not giving nearest Range
... Looks like that you are trying to annotate peaks. If that is the case, you might want to try the function annotatePeakInBatch in the ChIPpeakAnno package http://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html. Best regards, Julie Activity on a post you are following on support.bioco ...
written 6 months ago by Julie Zhu3.8k
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Answer: A: ATACseqQC needs too much memory
... Michael, The most recent version of ATACseqQC at http://bioconductor.org/packages/devel/bioc/html/ATACseqQC.html should run faster. Best regards, Julie ...
written 6 months ago by Julie Zhu3.8k
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Comment: C: ChIPpeakAnno binOverGene error
... Dear Wuze, Thanks for trying to run with the default setting and posting the session information! The current developer Jianhong is working on debugging and will keep you updated. Best regards, Julie On Nov 28, 2017, at 8:22 PM, wuzefeng2008 [bioc] <noreply@bioconductor.org<mailto:noreply@ ...
written 6 months ago by Julie Zhu3.8k
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Answer: A: ChIPpeakAnno binOverGene error
... Hi, could you please try with upstream.cutoff = 0, downstream.cutoff = 0? Also could you please provide your R session information by typing sessionInfo()? Thanks!   Best regards,   Julie ...
written 6 months ago by Julie Zhu3.8k
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Analyzing CIRCLE-seq data using GUIDEseq package
... Keith, GUIDEseq package can be used to analyze CIRCLE-seq too. During the preprocessing steps, you will not need to remove adaptors introduced in the GUIDE-seq protocol. In addition, you will need to set the max.R1.len =150 and max.R2.len = 150 using the GUIDEseqAnalysis function in GUIDEseq packag ...
guideseq circle-seq written 7 months ago by Julie Zhu3.8k
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Answer: A: CRISPRseek gRNA efficacy
... Joyce, Here is a description of the parameter useEfficacyFromInputSeq. Default FALSE. If set to TRUE, summary file will contain gRNA efficacy calculated from input sequences instead of from off-target analysis. Set it to TRUE if the input sequence is from a different species than the one used for o ...
written 7 months ago by Julie Zhu3.8k
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Comment: C: CRISPRseek CFD score
... Joyce, Glad to help! Great that you found the cause of problem. Thanks for letting me know! Best regards, Julie ...
written 7 months ago by Julie Zhu3.8k
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Comment: C: CRISPRseek CFD score
... Joyce, I tried offtarget analysis with your test sequence and human genome. I  was able to generate the InExon information. Here is the code snippet. Best regards, Julie    library(CRISPRseek)     library("BSgenome.Hsapiens.UCSC.hg19")     library(TxDb.Hsapiens.UCSC.hg19.knownGene)     librar ...
written 8 months ago by Julie Zhu3.8k

Latest awards to Julie Zhu

Popular Question 12 months ago, created a question with more than 1,000 views. For GEOquery
Scholar 12 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?
Scholar 12 months ago, created an answer that has been accepted. For A: createBarcodeFasta in GUIDEseq
Popular Question 12 months ago, created a question with more than 1,000 views. For CRISPRseek question on scoring
Popular Question 12 months ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Teacher 12 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 12 months ago, created an answer that has been accepted. For A: How to find nearest CpG islands around miRNA genes using granges?
Scholar 12 months ago, created an answer that has been accepted. For A: GUIDESeq analysis - handling biological and technical replicates
Scholar 12 months ago, created an answer that has been accepted. For A: offTargetAnalysis() Error in weights %*% mismatch.pos : non-conformable argument
Scholar 12 months ago, created an answer that has been accepted. For A: DistanceToNearest Not giving nearest Range
Popular Question 15 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 3.5 years ago, created an answer that has been accepted. For A: ChIPpeakAnno: Non-empty IRange object in case of no overlap
Autobiographer 3.8 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 3.8 years ago, created 100 posts.

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