User: Julie Zhu

gravatar for Julie Zhu
Julie Zhu3.8k
Reputation:
3,820
Status:
Trusted
Location:
United States
Website:
https://profiles.umass...
Last seen:
3 days, 2 hours ago
Joined:
8 years, 11 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 • 517 results • page 1 of 52 • next >
0
votes
2
answers
56
views
2
answers
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 days ago by Julie Zhu3.8k
0
votes
2
answers
56
views
2
answers
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 days ago by Julie Zhu3.8k
0
votes
2
answers
56
views
2
answers
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 4 days ago by Julie Zhu3.8k
0
votes
2
answers
56
views
2
answers
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 4 days ago by Julie Zhu3.8k
0
votes
1
answers
48
views
1
answers
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 13 days ago by Julie Zhu3.8k
0
votes
1
answers
54
views
1
answers
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 17 days ago by Julie Zhu3.8k
0
votes
1
answers
34
views
1
answers
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 5 weeks ago by Julie Zhu3.8k
0
votes
1
answers
75
views
1
answers
Answer: A: CFDscore calculations used in CRISPRseek
... Dawid, 1. Yes, “CFDscore” in CRISPRseek is calculated based on the table “NatureBiot2016SuppTable19DoenchRoot" (Doench et al., 2016) and Percent-Active column. 2. CFDscore is calculated using mismatch type and mismatch position although the mismatch activity is given as pos 20, 19, 18,....1 ...
written 5 weeks ago by Julie Zhu3.8k
0
votes
0
answers
136
views
0
answers
Job: Senior Bioinformatician position at University of Massachusetts Medical School, Worcester, MA
... Hi, We have a senior Bioinformatician/Computational Biologist position available at University of Massachusetts Medical School.  Please see the job description below. To apply online, please go to    https://www.ummsjobs.com/job/3124/ Thanks for your attention!   Kind regards,   Julie   OV ...
job see senior bioinformatician position written 3 months ago by Julie Zhu3.8k
0
votes
1
answers
73
views
1
answers
Answer: A: motif enrichment analysis for protein sequences
... Please take a look at https://www.bioconductor.org/packages/release/bioc/html/dagLogo.html and see if dagLogo fits your needs. Thanks! Best regards, Julie On Mar 6, 2018, at 9:58 PM, petyuk [bioc] <noreply@bioconductor.org<mailto:noreply@bioconductor.org>> wrote: Activity on a post y ...
written 4 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 16 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 3.6 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.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 230 users visited in the last hour