User: Julie Zhu

gravatar for Julie Zhu
Julie Zhu3.9k
Reputation:
3,850
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Location:
United States
Website:
https://profiles.umass...
Last seen:
6 days, 19 hours ago
Joined:
9 years, 6 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 • 535 results • page 1 of 54 • next >
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Answer: A: ChIPpeakAnno, MACS format annotation
... Lucy, Please try the following code snippet for importing the gtf file hg38_200000.gtf. library(refGenome) gtf = ensemblGenome() read.gtf(gtf, filename = "hg38_200000.gtf") genes = gtf@ev$genes[ ,c("gene_id","gene_name", "start", "end", "strand", "seqid")] annoData <- toGRanges(genes, format ...
written 8 days ago by Julie Zhu3.9k
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Comment: C: ChIPpeakAnno, MACS format annotation
... Lucy, Please send me the gtf file (julie.zhu@umassmed.edujulie.zhu@umassmed.edu). Thanks! BTW, I just noticed that you continued with an old thread which is about MACs format. Could you please start a new thread as ChIPpeakAnno::toGRanges GTF format instead to facilitate future searches? Thanks! B ...
written 8 days ago by Julie Zhu3.9k
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Comment: C: ChIPpeakAnno, MACS format annotation
... Lucy, Thanks for the clarification! Could you please post a few lines of the gtf annotation you used for analyzing your RNA-seq dataset? Thanks! Best regards, Julie ...
written 8 days ago by Julie Zhu3.9k
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Answer: A: ChIPpeakAnno, MACS format annotation
... Lucy, You mentioned that you downloaded the annotation file as GTF format from Ensembl. If this is correct, toGranges with format = "GFF" is not correct since GTF format is different from GFF format. Without changing your code, you could download the annotation file as a GFF file format instead. A ...
written 8 days ago by Julie Zhu3.9k
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Comment: C: ChIPpeakAnno, MACS format annotation
... Hi, You mentioned that you downloaded the annotation file as GTF format from Ensembl. If this is correct, toGranges with format = "GFF" is not correct since GTF format is different from GFF format. Without changing your code, could you please download the annotation file as a GFF file format instea ...
written 9 days ago by Julie Zhu3.9k
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Comment: C: CFDscore calculations used in CRISPRseek
... Hi Dawid, I tested the function with your input sequences and it ran fine at my end. I am not sure if the following post is helpful to you. https://github.com/cpsievert/pitchRx/issues/65 Best regards, Julie ...
written 7 weeks ago by Julie Zhu3.9k
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Comment: C: CFDscore calculations used in CRISPRseek
... Dawid, The summary file generated from running the new version 1.23.2 (git clone git.bioconductor.org:packages/CRISPRseek) should include both types of guides mappable or not mappable to a given genome.  Could you please try the following code snippets with the test input sequences? Thanks! librar ...
written 7 weeks ago by Julie Zhu3.9k
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Comment: C: CFDscore calculations used in CRISPRseek
... Dawid, I used the sequence you posted and it worked. I just realized that it would not work if you have a mixture of mappable and non-mappable guides. Could you please post the list of guides and code snippets you used for testing? Thanks! Best regards, Julie ...
written 7 weeks ago by Julie Zhu3.9k
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Comment: C: CFDscore calculations used in CRISPRseek
... Dawid, FYI, the current version works as long as there is at least one match with mismatch <= max.mismatch including perfect match. I have updated the package so that summary file will be generated even when there is no match found in the genome. Here is the command to download the most recent ...
written 8 weeks ago by Julie Zhu3.9k
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Comment: C: CFDscore calculations used in CRISPRseek
... Dear Dawid, Thanks for the great suggestion! I will add this feature in the dev version and keep you posted. Best, Julie ...
written 8 weeks ago by Julie Zhu3.9k

Latest awards to Julie Zhu

Popular Question 4 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 8 months ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Popular Question 8 months ago, created a question with more than 1,000 views. For GEOquery
Scholar 19 months ago, created an answer that has been accepted. For A: GUIDESeq analysis - handling biological and technical replicates
Scholar 19 months ago, created an answer that has been accepted. For A: offTargetAnalysis() Error in weights %*% mismatch.pos : non-conformable argument
Scholar 19 months ago, created an answer that has been accepted. For A: DistanceToNearest Not giving nearest Range
Teacher 19 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 19 months ago, created an answer that has been accepted. For A: How to find nearest CpG islands around miRNA genes using granges?
Scholar 19 months ago, created an answer that has been accepted. For A: createBarcodeFasta in GUIDEseq
Popular Question 19 months ago, created a question with more than 1,000 views. For CRISPRseek question on scoring
Popular Question 19 months ago, created a question with more than 1,000 views. For Biostrings::matchPattern,extract sequences
Popular Question 19 months ago, created a question with more than 1,000 views. For GEOquery
Scholar 19 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 22 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 4.1 years ago, created an answer that has been accepted. For A: ChIPpeakAnno: Non-empty IRange object in case of no overlap
Autobiographer 4.4 years ago, has more than 80 characters in the information field of the user's profile.
Centurion 4.4 years ago, created 100 posts.

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