User: Julie Zhu

gravatar for Julie Zhu
Julie Zhu4.0k
Reputation:
4,010
Status:
Trusted
Location:
United States
Website:
https://profiles.umass...
Last seen:
2 days, 9 hours ago
Joined:
9 years, 10 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 • 569 results • page 1 of 57 • next >
0
votes
1
answer
60
views
1
answers
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 18 days ago by Julie Zhu4.0k
1
vote
1
answer
60
views
1
answers
Answer: A: Genomic Coordinate Annoation
... You could try to use annotatePeakInBatch to annotate the regions by setting the parameter output to "overlapping" https://www.rdocumentation.org/packages/ChIPpeakAnno/versions/3.6.5/topics/annotatePeakInBatch For more information, please refer to http://bioconductor.org/packages/release/bioc/html/C ...
written 18 days ago by Julie Zhu4.0k
0
votes
1
answer
81
views
1
answers
Answer: A: How to align loci to in silico digested fragments
... Please take a look at the Bioconductor package REDseq (Restriction Enzyme Digestion followed by Sequencing) http://bioconductor.org/packages/release/bioc/html/REDseq.html. Hopefully this is what you are looking for. Best, Julie From: "emb13 [bioc]" noreply@bioconductor.org Reply-To: "reply+8f4f2e30 ...
written 6 weeks ago by Julie Zhu4.0k
0
votes
2
answers
764
views
2
answers
Comment: C: CRISPRseek scoring clarification
... Nan, Thanks for posting the code and gRNAs! FYI, CFD score of 1 means perfect match. Is it corret that the following two are the on-targets instead of off-targets? Do you find any off-targets for these two gRNAs? Thanks! I just ran your testing code and there is no offtarget found for either of ...
written 10 weeks ago by Julie Zhu4.0k
0
votes
2
answers
764
views
2
answers
Comment: C: CRISPRseek scoring clarification
... Nan, A great question! Could you please look at one of the output files offTargets.xls to compare the two gRNAs and their offTargets to see if there are any differences in terms of their offTargets? If it is still hard to distinguish these two cases, could you please post the two gRNA sequences an ...
written 10 weeks ago by Julie Zhu4.0k
0
votes
0
answers
88
views
0
answers
Comment: C: My post or response to post does not get sent to the Bioconductor email list
... Thanks so much, Lori! FYI, I posted the issue at github a couple of weeks ago. Best regards, Julie ...
written 11 weeks ago by Julie Zhu4.0k
0
votes
2
answers
117
views
2
answers
Comment: C: Unable to generate feature vector with custom genome in cleanUpdTSeq
... Danielle, You will need to remove anything after | and any spaces before that. For example, use GLCHR01 to replace “ GLCHR01 | organism=GiardiaAssemblageAisolateWB | version=2013-02-08 | length=1491578 | SO=chromosome =2013-02-08 | length=863 | SO=supercontig” Best, Julie ...
written 11 weeks ago by Julie Zhu4.0k
0
votes
2
answers
117
views
2
answers
Comment: C: Unable to generate feature vector with custom genome in cleanUpdTSeq
... Danielle, I believe your guess is correct, i.e., it reads the chromosome names directly from the fasta file provided. There are probably issues with the fasta file itself. You can open the fasta file to see what is the first line. Alternatively, you can use grep to find all the chromosome names in ...
written 11 weeks ago by Julie Zhu4.0k
0
votes
0
answers
88
views
0
answers
My post or response to post does not get sent to the Bioconductor email list
... Hi, I am still have problem with my posts or response to others' post, i.e., my posts are not being sent out to the Bioconductor email list. Could you please help? Thanks! Best regards, Julie ...
posts email written 11 weeks ago by Julie Zhu4.0k
0
votes
2
answers
117
views
2
answers
Comment: C: Unable to generate feature vector with custom genome in cleanUpdTSeq
... Danielle, If you look at the seqnames column, you will see that your peak ranges are located in different chromosomes such as GLCHR03 and GL50803. In order to obtain sequence from these different chromosomes, the BSgenome needs to have the matched chromosome name. Dose it make sense? Thanks! Be ...
written 11 weeks ago by Julie Zhu4.0k

Latest awards to Julie Zhu

Popular Question 4 months ago, created a question with more than 1,000 views. For CRISPRseek question on scoring
Popular Question 4 months ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Scholar 4 months ago, created an answer that has been accepted. For A: createBarcodeFasta in GUIDEseq
Popular Question 8 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 12 months ago, created a question with more than 1,000 views. For GEOquery
Popular Question 12 months ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Scholar 23 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 23 months ago, created a question with more than 1,000 views. For CRISPRseek question on scoring
Popular Question 23 months ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Popular Question 23 months ago, created a question with more than 1,000 views. For GEOquery
Scholar 23 months ago, created an answer that has been accepted. For A: createBarcodeFasta in GUIDEseq
Teacher 23 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 23 months ago, created an answer that has been accepted. For A: How to find nearest CpG islands around miRNA genes using granges?
Scholar 23 months ago, created an answer that has been accepted. For A: GUIDESeq analysis - handling biological and technical replicates
Scholar 23 months ago, created an answer that has been accepted. For A: offTargetAnalysis() Error in weights %*% mismatch.pos : non-conformable argument
Scholar 23 months ago, created an answer that has been accepted. For A: DistanceToNearest Not giving nearest Range
Popular Question 2.2 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 4.4 years ago, created an answer that has been accepted. For A: ChIPpeakAnno: Non-empty IRange object in case of no overlap
Autobiographer 4.7 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 4.7 years ago, created 100 posts.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 125 users visited in the last hour