Moderator: Madelaine Gogol

gravatar for Madelaine Gogol
Madelaine Gogol5.0k
Reputation:
4,950
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Trusted
Location:
Kansas City
Website:
http://research.stower...
Twitter:
@mmarchin
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Google Scholar Page
Last seen:
1 month, 3 weeks ago
Joined:
8 years, 4 months 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 • 271 results • page 1 of 28 • next >
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Comment: C: lack of replicates in single-cell RNA-seq
... Huh, what would I do if I had a replicate! That would be cool! See if the clusters look "the same", I suppose, but if they don't, then what? Hmmmmmmm... ...
written 8 weeks ago by Madelaine Gogol5.0k
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Comment: C: which is good to study methylation among breast cancer patients; ChIP-Seq and Wh
... This feels more like a biology question... You may try seqanswers.com? I guess it depends on which aspects are more important to you, methylation or histone marks or what. You may be able to find some public data to get you started. ...
written 9 weeks ago by Madelaine Gogol5.0k
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Comment: C: Sequencing with 10X genomics
... You might want to look at http://10xqc.com/ ...
written 4 months ago by Madelaine Gogol5.0k
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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 4 months ago by Madelaine Gogol5.0k
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Comment: C: Classify cells using seurat
... I have used SetIdent() to do something like that. ...
written 4 months ago by Madelaine Gogol5.0k
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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 5 months ago by Madelaine Gogol5.0k
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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 5 months ago by Madelaine Gogol5.0k
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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 5 months ago by Madelaine Gogol5.0k
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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 8 months ago by Madelaine Gogol5.0k
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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 8 months ago by Madelaine Gogol5.0k

Latest awards to Madelaine Gogol

Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Biology Database Project
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Scholar 9 months ago, created an answer that has been accepted. For A: Running and Analyzing fastqc on multiple fastq files
Popular Question 18 months ago, created a question with more than 1,000 views. For Entice Biologists To Learn R
Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Commentator 23 months ago, created a comment with at least 3 up-votes. For C: Biology Database Project
Great Question 23 months ago, created a question with more than 5,000 views. For Nextseq for analysts
Prophet 2.0 years ago, created a post with more than 20 followers. For What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
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)
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Great Question 2.4 years ago, created a question with more than 5,000 views. For What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
Appreciated 2.4 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 2.7 years ago, created a question with more than 1,000 views. For Entice Biologists To Learn R
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Entice Biologists To Learn R
Commentator 2.9 years ago, created a comment with at least 3 up-votes. For C: Which Bachelor Should I Choose For A Position In Bioinformatics?
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Scholar 3.2 years ago, created an answer that has been accepted. For A: Running and Analyzing fastqc on multiple fastq files

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