Moderator: David Quigley

gravatar for David Quigley
David Quigley11k
Reputation:
10,550
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Trusted
Location:
San Francisco
Website:
http://davidquigley.com
Last seen:
2 weeks, 5 days ago
Joined:
8 years 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 9 months ago by David Quigley11k
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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 months ago by David Quigley11k
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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 2.4 years ago by David Quigley11k
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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 2.5 years ago by David Quigley11k
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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 2.6 years ago by David Quigley11k
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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 2.6 years ago by David Quigley11k
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Comment: C: Identify somatic mutations in cancer exome without a matched pair.
... Thanks for these notes, very helpful. ...
written 2.7 years ago by David Quigley11k
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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 2.7 years ago by David Quigley11k
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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 2.7 years ago by David Quigley11k
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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 2.7 years ago by David Quigley11k

Latest awards to David Quigley

Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: What Do You Use For Publication Alerts?
Appreciated 7 weeks ago, created a post with more than 5 votes. For C: Minimal Accepted Works In Bioinformatics Journals
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Why Are Almost All Protein Or Mrna Abundance Measures Transformed By Log?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: What Do You Use For Publication Alerts?
Scholar 6 months ago, created an answer that has been accepted. For A: Looking for gene expression data from cultured human cells treated with drugs
Popular Question 6 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?
Popular Question 6 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?
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: When It'S A Sequence And When It'S Not?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: What Do You Use For Publication Alerts?
Great Question 11 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 12 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 12 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 13 months ago, created a post with more than 25 bookmarks. For A: What Is The Best Pipeline For Human Whole Exome Sequencing?
Appreciated 16 months ago, created a post with more than 5 votes. For C: Minimal Accepted Works In Bioinformatics Journals
Good Question 16 months ago, asked a question that was upvoted at least 5 times. For Alternatives To Caarray For Microarray Storage
Popular Question 16 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 18 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
Appreciated 20 months ago, created a post with more than 5 votes. For C: Minimal Accepted Works In Bioinformatics Journals
Good Answer 21 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 23 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 23 months ago, created an answer with at least 3 up-votes. For A: What Do You Use For Publication Alerts?
Appreciated 23 months ago, created a post with more than 5 votes. For C: Minimal Accepted Works In Bioinformatics Journals
Great Question 23 months ago, created a question with more than 5,000 views. For Bulk Download Of Ncbi Gene "Summary" Field
Popular Question 2.0 years ago, created a question with more than 1,000 views. For How To Transform Microarray Data To Adjust For Batch Effects

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