Moderator: Madelaine Gogol

gravatar for Madelaine Gogol
Madelaine Gogol4.9k
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4,940
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Trusted
Location:
Kansas City
Website:
http://research.stower...
Twitter:
@mmarchin
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Google Scholar Page
Last seen:
3 weeks, 6 days ago
Joined:
8 years, 1 month ago
Email:
m********@gmail.com

I'm a Programmer Analyst in a bioinformatics core facility at Stowers Institute. I use R (and Perl, don't judge me) to munge and analyze data from all sorts of critters in all sorts of (usually sequencing) experiments.

Posts by Madelaine Gogol

<prev • 269 results • page 1 of 27 • next >
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Comment: C: Sequencing with 10X genomics
... You might want to look at http://10xqc.com/ ...
written 5 weeks ago by Madelaine Gogol4.9k
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Job: Programmer Analyst job(s) in Kansas City at Stowers Institute
... The Computational Biology Core at Stowers Institute will be hiring 3 Programmer Analysts this year. Stowers is a wonderful place to work with scientists studying all sorts interesting of basic research questions in a variety of model organisms. We are often pushing the boundaries of technology and e ...
R kansas city sequencing job linux written 5 weeks ago by Madelaine Gogol4.9k
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Comment: C: Classify cells using seurat
... I have used SetIdent() to do something like that. ...
written 8 weeks ago by Madelaine Gogol4.9k
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Comment: C: technical problem with R and GO terms
... Yep, something like: findreplace<-function(df) { df[,3] <- NA df[grepl("GO:002", df[,1]),3] <- c("yes") df[!grepl("GO:002", df[,1]),3] <- c("no") df } list_of_df <- list(df1,df2,df3) fixed_list <- lapply(list_of_df,findreplace) ...
written 9 weeks ago by Madelaine Gogol4.9k
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Comment: C: RNAseq and ChIPseq integration
... A broad question deserves a broad answer. Venn diagrams and heatmaps. : D Okay, that was a bit snarky. One thing you could consider to start with is the overlap between differentially regulated genes and genes with ChIP-seq peaks... And whether that overlap is more than you would expect by chance. ...
written 10 weeks ago by Madelaine Gogol4.9k
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Comment: C: pathway for single cell RNA-seq
... Biologists around here seem to like IPA, but I haven't tried it myself. ...
written 3 months ago by Madelaine Gogol4.9k
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Comment: C: Has anyone tried to run SNPEff, Bedtools or Prokka with GNU parallel or a simila
... You may find [Pierre Lindenbaum's tutorial on parallel useful][1]. [1]: https://s3-eu-west-1.amazonaws.com/pfigshare-u-files/1235681/parallel01.pdf ...
written 5 months ago by Madelaine Gogol4.9k
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Comment: C: nanopore-Illumina hybrid RNA assembly
... I recently heard of someone using Pilon for something similar, might be another option to consider. There are a few posts on the nanopore community about it. ...
written 6 months ago by Madelaine Gogol4.9k
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Comment: C: Drawing Venn Diagram
... Maybe consider [UpSetR][1]? [1]: https://github.com/hms-dbmi/UpSetR ...
written 7 months ago by Madelaine Gogol4.9k
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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 14 months ago by Madelaine Gogol4.9k

Latest awards to Madelaine Gogol

Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Biology Database Project
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Scholar 6 months ago, created an answer that has been accepted. For A: Running and Analyzing fastqc on multiple fastq files
Popular Question 15 months ago, created a question with more than 1,000 views. For Entice Biologists To Learn R
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: Biology Database Project
Great Question 20 months ago, created a question with more than 5,000 views. For Nextseq for analysts
Prophet 22 months ago, created a post with more than 20 followers. For What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
Good Answer 22 months ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Appreciated 2.1 years ago, created a post with more than 5 votes. For A: What Are The Bioinformatics-Related Aliases Or Functions In Your Bashrc
Great Question 2.1 years ago, created a question with more than 5,000 views. For What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
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 2.4 years ago, created a question with more than 1,000 views. For Entice Biologists To Learn R
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Entice Biologists To Learn R
Commentator 2.6 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 2.7 years ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
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Teacher 2.8 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 2.8 years ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Good Answer 2.8 years ago, created an answer that was upvoted at least 5 times. For A: What Methods Do You Use For Short Read Mapping?
Teacher 2.8 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
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Popular Question 2.9 years ago, created a question with more than 1,000 views. For Entice Biologists To Learn R
Appreciated 2.9 years ago, created a post with more than 5 votes. For A: What Are The Bioinformatics-Related Aliases Or Functions In Your Bashrc
Scholar 3.0 years ago, created an answer that has been accepted. For A: Running and Analyzing fastqc on multiple fastq files

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