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User: Gareth Palidwor

gravatar for Gareth Palidwor
Gareth Palidwor • 1.6k
Reputation:
1,570
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Trusted
Location:
Ottawa
Website:
http://www.perkinslab....
Last seen:
5 months, 2 weeks ago
Joined:
10 years, 2 months ago
Email:
g********@yahoo.com

I'm a Research Assistant at the Ottawa Hospital Research Institute

Posts by Gareth Palidwor

<prev • 63 results • page 1 of 7 • next >
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Comment: C: Using PAcalls for Clariom chips
... Hi Kris: Did you ever get a solution to this? I'm having similar issues with the Clariom D mouse array. paCalls(ClariomMouseData) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘paCalls’ for signature ‘"HTAFeatureSet"’ ...
written 2.7 years ago by Gareth Palidwor • 1.6k
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Comment: C: Subtracting contamination from RNASeq data
... I got an answer for this from Michael Love on the Bioconductor support forum: > So you could put it in the model as a numeric covariate (you don't do > anything special just put it in the design). This however assumes the > relationship with expression is log linear (so linear with log > ...
written 2.9 years ago by Gareth Palidwor • 1.6k
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Comment: C: Subtracting contamination from RNASeq data
... Hi Bruce: Removing a scaled percentage of MEF reads based on the contamination level estimate is straightforward and I've done that however, it messes up the fold change analysis. Subtraction will increase the expression variance by varying amounts per gene and that information is lost when I gen ...
written 3.0 years ago by Gareth Palidwor • 1.6k
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Comment: C: Subtracting contamination from RNASeq data
... Bruce: Thanks for your response, clarification added above in the original post. The differentiating cell line is also mouse so I can't remove the contamination by mapping. ...
written 3.0 years ago by Gareth Palidwor • 1.6k
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Subtracting contamination from RNASeq data
... I have a set of RNASeq data for various points of a differentiation time series, with replicates. A known fraction of the cells in each sample are MEFs, and that fraction varies quite a bit per sample. I have expression data for a pure MEF sample grown under similar conditions. I'd like to do a fo ...
rna-seq written 3.0 years ago by Gareth Palidwor • 1.6k • updated 3.0 years ago by h.mon ♦ 30k
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Answer: A: Is There A Database Of Known Dna Binding Proteins?
... DNA binding is identified by the Gene Ontology annotations GO:0003677 Many protein databases have GO annotations that you can filter by. ...
written 8.3 years ago by Gareth Palidwor • 1.6k
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Answer: A: Functional Roles Of At-Rich Regions And Gc-Rich Regions In Mammalian Genomes?
... I don't think you're going to find a "database" of functional roles of AT and GC rich regions as the GC bias of a region is just a broad property of a sequence. Bad analogy, but it would be like trying to find a database of things in the world by weight. ...
written 8.3 years ago by Gareth Palidwor • 1.6k
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Answer: A: List Of Organization That Are Looking For Freelancer Bioinformatics, Genetics Or
... Bioinformatics freelancing/consulting been discussed previously on BioStar: - https://www.biostars.org/p/5016/ - https://www.biostars.org/p/1449/ ...
written 8.3 years ago by Gareth Palidwor • 1.6k • updated 10 months ago by zx8754 ♦ 9.3k
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Answer: A: Appropriate Podcasts For A Bioinformatician?
... For general science podcasts, I'd recommend Quirks and Quarks from the Canadian Broadcasting Corporation: http://www.cbc.ca/quirks/ ...
written 8.3 years ago by Gareth Palidwor • 1.6k
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Answer: A: Biomart: Finding Ensembl Repeat Regions In A List Of Coordinates From R
... The simplest way would be to download a list of RepeatMasker determined repeat ranges from UCSC Table Browser, then intersect those with your set of regions using IRanges. It's not clear what genome you're using but UCSC has repeat regions for quite a few. **edited; accidentally said BioMart instead ...
written 8.3 years ago by Gareth Palidwor • 1.6k

Latest awards to Gareth Palidwor

Popular Question 5 months ago, created a question with more than 1,000 views. For Subtracting contamination from RNASeq data
Scholar 5 months ago, created an answer that has been accepted. For A: Local Copy Of Pubmed
Popular Question 2.6 years ago, created a question with more than 1,000 views. For Subtracting contamination from RNASeq data
Scholar 2.6 years ago, created an answer that has been accepted. For A: Local Copy Of Pubmed
Appreciated 8.3 years ago, created a post with more than 5 votes. For C: Biological Molecules For Which There Are No Databases
Appreciated 8.3 years ago, created a post with more than 5 votes. For A: Best Hardware Solution For Medium-Size Bioinformatics Lab [15-20 Computers]
Appreciated 8.3 years ago, created a post with more than 5 votes. For A: What Kind Of Bioinformatics Tutorials Would You Like To See Online?
Appreciated 8.3 years ago, created a post with more than 5 votes. For A: Bioinformatics Ninja Or Samurai Or Rock-Star
Appreciated 8.3 years ago, created a post with more than 5 votes. For A: Help Me Understand Why So Many Reads Do Not Align!
Appreciated 8.3 years ago, created a post with more than 5 votes. For A: How To Map Ensembl Exon Ids To Gene Ids?
Appreciated 8.3 years ago, created a post with more than 5 votes. For A: What Are The Most Common Stupid Mistakes In Bioinformatics?
Appreciated 8.3 years ago, created a post with more than 5 votes. For A: How Do You Acknowledge Biostar And Its Contributors In Your Research Output?
Appreciated 8.3 years ago, created a post with more than 5 votes. For A: Local Copy Of Pubmed
Appreciated 8.3 years ago, created a post with more than 5 votes. For A: R And Ape Vs Bioperl
Good Answer 8.3 years ago, created an answer that was upvoted at least 5 times. For A: What Kind Of Bioinformatics Tutorials Would You Like To See Online?
Good Answer 8.3 years ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics Ninja Or Samurai Or Rock-Star
Good Answer 8.3 years ago, created an answer that was upvoted at least 5 times. For A: Help Me Understand Why So Many Reads Do Not Align!
Good Answer 8.3 years ago, created an answer that was upvoted at least 5 times. For A: How To Map Ensembl Exon Ids To Gene Ids?
Good Answer 8.3 years ago, created an answer that was upvoted at least 5 times. For A: What Are The Most Common Stupid Mistakes In Bioinformatics?
Good Answer 8.3 years ago, created an answer that was upvoted at least 5 times. For A: How Do You Acknowledge Biostar And Its Contributors In Your Research Output?
Good Answer 8.3 years ago, created an answer that was upvoted at least 5 times. For A: R And Ape Vs Bioperl
Guru 8.3 years ago, received more than 100 upvotes.
Voter 8.3 years ago, voted more than 100 times.
Scholar 8.3 years ago, created an answer that has been accepted. For A: Local Copy Of Pubmed
Supporter 8.3 years ago, voted at least 25 times.
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