Moderator: David Quigley

gravatar for David Quigley
David Quigley10k
Reputation:
10,450
Status:
Trusted
Location:
San Francisco
Website:
http://davidquigley.com
Last seen:
4 weeks, 1 day ago
Joined:
7 years, 4 months ago
Email:
d**************@gmail.com

I am a cancer genetics researcher at UCSF. My work in Allan Balmain's lab centers on using analytical methods to identify genetic networks associated with susceptibility to cancer or which are selectively modified after a tumor develops. We primarily use mouse models of skin and lung cancer. My training is in Computer Science and Biomedical Informatics; I also have worked as a professional software developer.

Posts by David Quigley

<prev • 433 results • page 1 of 44 • next >
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Comment: C: spreadsheet tools alternative
... Renesh's comment is not correct. Try the following: Open a worksheet. Type "MAR7". You'll see "7-Mar" as Excel formats your text as a date. Now correct the formatting to "text" (Format|Cells). You will see "7-Mar" become a number. On my Macintosh it's 42801. There is no way to recover the original t ...
written 8 weeks ago by David Quigley10k
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Comment: C: Where can I get ?or how can I make a mappability track for hg38 assembly
... As of September 2017 the gem-mappability binary is missing from the GEM build. The note on the GEM wiki dated 2012 states "mappability tools are still in the process of being migrated to the new mapping engine. The mappability will come back online shortly." ([wiki for the GEM library][1]). There is ...
written 10 weeks ago by David Quigley10k
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Answer: A: BinGo customerized work flow
... The ontology file describes the structure of the ontology tree. It has three root nodes (Biological Process, Molecular Function, Cellular Compartment) and gets more specific from there, e.g. "M phase mitosis". It does not link any particular gene to an ontology entry. The Annotation file indicates w ...
written 21 months ago by David Quigley10k
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Job: UCSF Bioinformatics Junior Specialist, Helen Diller Cancer Center
... University of California, San Francisco Department of Obstetrics, Gynecology, and Reproductive Sciences Division of Gynecologic Oncology Junior Specialist Search The UCSF Department of Obstetrics, Gynecology, and Reproductive Sciences, Division of Gynecologic Oncology, is recruiting for Non-Faculty ...
immunology next-gen job rna-seq written 22 months ago by David Quigley10k
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Comment: C: bioinformatics conference ranking
... [(days distant from winter solstice) x latitude x (distance in km from college roommate)] / [(registration cost) * (number of concurrent tracks)] ...
written 23 months ago by David Quigley10k
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Answer: A: EGFR and KRAS expression
... If you don't specifically need RNA-seq data, there's a very large amount of retrospective transcriptome data on GEO, e.g. http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE40967 http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68468 http://www.ncbi.nlm.nih.gov/gds/?term=colon%20cancer You c ...
written 24 months ago by David Quigley10k
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Comment: C: Identify somatic mutations in cancer exome without a matched pair.
... Thanks for these notes, very helpful. ...
written 2.0 years ago by David Quigley10k
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Comment: C: Is the PAM50 subtype available for TCGA BRCA data?
... @kanwarjag: I assume your answer is meant as a comment to my answer above; if so, please leave it as a comment next time rather than posting an answer to the question. What I mean by "somewhat different results for edge case tumors" is that, in practice, when you use genefu to assign PAM50 classes, ...
written 2.0 years ago by David Quigley10k
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Answer: A: Get number of variations in a huge VCF using Tabix?
... Heng Li says no, and he should know: >> Dear Heng, >> >> We are wondering if there’s a fast approach to use tabix or any other hack to get the total number of variants that a VCF has without actually reading the whole vcf file and counting the lines. I assume that the total numbe ...
written 2.0 years ago by David Quigley10k
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Answer: A: Is the PAM50 subtype available for TCGA BRCA data?
... You'll find a list derived from microrarrays (Nature 2012 release) at https://tcga-data.nci.nih.gov/docs/publications/brca_2012/ specifically http://tcga-data.nci.nih.gov/docs/publications/brca_2012/BRCA.547.PAM50.SigClust.Subtypes.txt It appears that there is no canonical PAM50 call set for the ...
written 2.0 years ago by David Quigley10k

Latest awards to David Quigley

Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: When It'S A Sequence And When It'S Not?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: What Do You Use For Publication Alerts?
Great Question 3 months ago, created a question with more than 5,000 views. For How Many Reads In A Bam File Are Aligned To An Arbitrary Region
Popular Question 4 months ago, created a question with more than 1,000 views. For What are the output values for PICNIC when called from the binary build?
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Networks: Fastest Way To Define Cliques And Connectors Between Them For Large Da
Gold Standard 5 months ago, created a post with more than 25 bookmarks. For A: What Is The Best Pipeline For Human Whole Exome Sequencing?
Appreciated 8 months ago, created a post with more than 5 votes. For C: Minimal Accepted Works In Bioinformatics Journals
Good Question 8 months ago, asked a question that was upvoted at least 5 times. For Alternatives To Caarray For Microarray Storage
Popular Question 8 months ago, created a question with more than 1,000 views. For Microarray Dataset Formats: What Should My Program Know How To Read?
Good Answer 10 months ago, created an answer that was upvoted at least 5 times. For A: Networks: Fastest Way To Define Cliques And Connectors Between Them For Large Da
Appreciated 10 months ago, created a post with more than 5 votes. For C: Minimal Accepted Works In Bioinformatics Journals
Appreciated 12 months ago, created a post with more than 5 votes. For C: Minimal Accepted Works In Bioinformatics Journals
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: Networks: Fastest Way To Define Cliques And Connectors Between Them For Large Da
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Networks: Fastest Way To Define Cliques And Connectors Between Them For Large Da
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: What Do You Use For Publication Alerts?
Appreciated 15 months ago, created a post with more than 5 votes. For C: Minimal Accepted Works In Bioinformatics Journals
Great Question 15 months ago, created a question with more than 5,000 views. For Bulk Download Of Ncbi Gene "Summary" Field
Popular Question 16 months ago, created a question with more than 1,000 views. For How To Transform Microarray Data To Adjust For Batch Effects
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: Networks: Fastest Way To Define Cliques And Connectors Between Them For Large Da
Appreciated 18 months ago, created a post with more than 5 votes. For C: Minimal Accepted Works In Bioinformatics Journals
Popular Question 18 months ago, created a question with more than 1,000 views. For Quickest Way To Pull A List Of Reads Out Of A Bam File?
Appreciated 19 months ago, created a post with more than 5 votes. For C: Minimal Accepted Works In Bioinformatics Journals
Popular Question 21 months ago, created a question with more than 1,000 views. For Generating Summary Statistics And Coverage Plots From Illumina Ga2 Data
Commentator 23 months ago, created a comment with at least 3 up-votes. For C: When It'S A Sequence And When It'S Not?
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: Bulk Download Of Ncbi Gene "Summary" Field

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