Moderator: Madelaine Gogol

gravatar for Madelaine Gogol
Madelaine Gogol4.8k
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Location:
Kansas City
Website:
http://research.stower...
Twitter:
@mmarchin
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Google Scholar Page
Last seen:
5 days, 3 hours ago
Joined:
7 years, 6 months ago
Email:
m********@gmail.com

I'm a Programmer in a bioinformatics core facility at a research institute. I use R and Perl to munge and analyze data from "next-generation" sequencing experiments and microarrays.

Posts by Madelaine Gogol

<prev • 261 results • page 1 of 27 • next >
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Comment: C: Drawing Venn Diagram
... Maybe consider [UpSetR][1]? [1]: https://github.com/hms-dbmi/UpSetR ...
written 16 days ago by Madelaine Gogol4.8k
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Comment: C: Circos and RNA-Seq Data
... Did you see http://circos.ca/tutorials/lessons/ ? It's not a quick and easy tool to use, and requires some investment of time... ...
written 7 months ago by Madelaine Gogol4.8k
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Comment: C: Help with NGS analysis
... If you want to learn more about bioinformatics and analysis, you might take a look at the (in development) [Biostars handbook][1] [1]: https://www.biostarhandbook.com/ ...
written 8 months ago by Madelaine Gogol4.8k
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Comment: C: Can I design a Circos image without an existent genome reference?
... You have a reference genome, it is your de novo assembly, however draft it may be. It may have lots of scaffolds, but you can use it as if it was a regular genome. You will just have to do some extra work to get it set up with circos. ...
written 8 months ago by Madelaine Gogol4.8k
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Comment: C: Establishing a Core Bioinformatics Facility
... You may be interested in [Establishing a Successful Bioinformatics Core Facility Team][1] or [bioinfo-core.org][2]. Good luck! [1]: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000368 [2]: http://bioinfo-core.org/index.php/Main_Page ...
written 11 months ago by Madelaine Gogol4.8k
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Comment: C: Running and Analyzing fastqc on multiple fastq files
... Visiting from the future... If anyone is dealing with this issue, they may also want to check out [MultiQC][1]. [1]: http://multiqc.info/ ...
written 11 months ago by Madelaine Gogol4.8k
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Comment: C: What do you work on while waiting on your programs to finish?
... Plan another KC Bioinformatics meetup (J/K). : ) Try and make the argument for more computational resources! Ha ha. But seriously, those are all good options. Learning new keyboard shortcuts? ...
written 12 months ago by Madelaine Gogol4.8k
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Comment: C: Heatmaps in R
... Don't forget aheatmap from the NMF package. I also often roll my own with image() and layout(), and it is TERRIBLE! ...
written 13 months ago by Madelaine Gogol4.8k
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Comment: C: Advice for someone considering bioinformatics?
... An online course might be a good way to get started: https://www.edx.org/xseries/data-analysis-life-sciences https://www.coursera.org/specializations/jhu-data-science I have an intro to R course for biologists that is kinda old, but could be a super entry level thing to take a look at: https://gi ...
written 16 months ago by Madelaine Gogol4.8k
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Comment: C: Advice for someone considering bioinformatics?
... I would try to get your hands on some data and attempt to do something with it in R, answer a question that you have. This may force you to improve your R knowledge. Getting the data into shape, depending on the type of data and where you get it from -- might make you want to learn a bit more comman ...
written 18 months ago by Madelaine Gogol4.8k

Latest awards to Madelaine Gogol

Popular Question 8 months ago, created a question with more than 1,000 views. For Entice Biologists To Learn R
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: Biology Database Project
Great Question 13 months ago, created a question with more than 5,000 views. For Nextseq for analysts
Prophet 15 months ago, created a post with more than 20 followers. For What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Appreciated 18 months ago, created a post with more than 5 votes. For A: What Are The Bioinformatics-Related Aliases Or Functions In Your Bashrc
Great Question 18 months ago, created a question with more than 5,000 views. For What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
Appreciated 19 months ago, created a post with more than 5 votes. For A: What Are The Bioinformatics-Related Aliases Or Functions In Your Bashrc
Popular Question 22 months ago, created a question with more than 1,000 views. For Entice Biologists To Learn R
Popular Question 22 months ago, created a question with more than 1,000 views. For Entice Biologists To Learn R
Commentator 2.1 years ago, created a comment with at least 3 up-votes. For C: Which Bachelor Should I Choose For A Position In Bioinformatics?
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: What Are The Bioinformatics-Related Aliases Or Functions In Your Bashrc
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: What Are The Bioinformatics-Related Aliases Or Functions In Your Bashrc
Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: What Methods Do You Use For Short Read Mapping?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: The Easiest/Fastest Way To Get From Bam To Tpm Or Rpkm
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: What Are The Bioinformatics-Related Aliases Or Functions In Your Bashrc
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Entice Biologists To Learn R
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: What Are The Bioinformatics-Related Aliases Or Functions In Your Bashrc
Scholar 2.4 years ago, created an answer that has been accepted. For A: Running and Analyzing fastqc on multiple fastq files
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: The Easiest/Fastest Way To Get From Bam To Tpm Or Rpkm
Good Answer 2.6 years ago, created an answer that was upvoted at least 5 times. For A: How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: How To Assess The Quality Of An Assembly? (Is There No Magic Formula?)

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