Moderator: Madelaine Gogol

gravatar for Madelaine Gogol
Madelaine Gogol4.8k
Reputation:
4,850
Status:
Trusted
Location:
Kansas City
Website:
http://research.stower...
Twitter:
@mmarchin
Scholar ID:
Google Scholar Page
Last seen:
7 minutes ago
Joined:
7 years, 8 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 • 263 results • page 1 of 27 • next >
0
votes
2
answers
158
views
2
answers
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 14 days ago by Madelaine Gogol4.8k
0
votes
0
answers
163
views
0
answers
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 28 days ago by Madelaine Gogol4.8k
0
votes
1
answer
207
views
1
answers
Comment: C: Drawing Venn Diagram
... Maybe consider [UpSetR][1]? [1]: https://github.com/hms-dbmi/UpSetR ...
written 10 weeks ago by Madelaine Gogol4.8k
0
votes
0
answers
557
views
0
answers
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 9 months ago by Madelaine Gogol4.8k
2
votes
1
answer
470
views
1
answers
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 10 months ago by Madelaine Gogol4.8k
0
votes
1
answer
388
views
1
answers
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 10 months ago by Madelaine Gogol4.8k
2
votes
5
answers
819
views
5
answers
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 13 months ago by Madelaine Gogol4.8k
1
vote
2
answers
11k
views
2
answers
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 13 months ago by Madelaine Gogol4.8k
1
vote
0
answers
470
views
0
answers
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 14 months ago by Madelaine Gogol4.8k
0
votes
0
answers
3.2k
views
0
answers
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 15 months ago by Madelaine Gogol4.8k

Latest awards to Madelaine Gogol

Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Scholar 5 weeks ago, created an answer that has been accepted. For A: Running and Analyzing fastqc on multiple fastq files
Popular Question 10 months ago, created a question with more than 1,000 views. For Entice Biologists To Learn R
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Great Question 15 months ago, created a question with more than 5,000 views. For Nextseq for analysts
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Biology Database Project
Prophet 16 months ago, created a post with more than 20 followers. For What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
Good Answer 17 months ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Appreciated 20 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 20 months ago, created a question with more than 5,000 views. For What Is Your Favorite Question To Ask When Interviewing Potential Bioinformaticians?
Appreciated 21 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 24 months ago, created a question with more than 1,000 views. For Entice Biologists To Learn R
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Entice Biologists To Learn R
Commentator 2.2 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 2.2 years ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Teacher 2.3 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 2.3 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 2.3 years ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Good Answer 2.3 years ago, created an answer that was upvoted at least 5 times. For A: What Methods Do You Use For Short Read Mapping?
Teacher 2.3 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 2.4 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 2.4 years ago, created a question with more than 1,000 views. For Entice Biologists To Learn R
Appreciated 2.5 years ago, created a post with more than 5 votes. For A: What Are The Bioinformatics-Related Aliases Or Functions In Your Bashrc
Scholar 2.5 years ago, created an answer that has been accepted. For A: Running and Analyzing fastqc on multiple fastq files
Teacher 2.7 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

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1515 users visited in the last hour