User: paul.e.gradie

gravatar for paul.e.gradie
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60
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Location:
Australia/Melbourne/University of Melbourne
Twitter:
@paul_gradie
Last seen:
8 months ago
Joined:
1 year, 9 months ago
Email:
p************@gmail.com

I'm looking for a post doc in Melbourne, Aus where I can contribute to bioinformatic work and next gen data analysis!

Contact me if you are in need of large data set analysis skills!

 

Posts by paul.e.gradie

<prev • 9 results • page 1 of 1 • next >
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Answer: A: Machine Learning - RNAseq
... So many months ago! Sorry this wasn't seen sooner - I'm sure you've resolved this problem already. Google tools such as HTseq and SubRead. These are packages that contain tools for quantifying read counts, which are then commonly used for downstream analysis. HTseq-Count and featureCounts in partic ...
written 8 months ago by paul.e.gradie60
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Answer: A: How to access GeneCards via XML?
... This is old, but there are over 500 views so I'll add an answer - GeneCards seems to be a privately curated information repository. It is useful, but they charge a fee for allowing access to their database (if you are a commercial user). Making the data base available to the public and parsable as ...
written 12 months ago by paul.e.gradie60
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Change linetype (or other plot properties) in ggplot made by some R package
... Hi all, I'm working my way through R to become a pro at visualizing data, and I'm stuck on something that I think is probably very simple. I'll describe my current problem, but just so that everyone knows - the answers here should be applicable to many other similar problems. Apologies in advance ...
R plot ggplot graphing written 15 months ago by paul.e.gradie60
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Answer: A: Chance: Comprehensive Software For Quality Control And Validation Of Chip-Seq Da
... Wow - no updates to this? Who is going to use this if it can't accommodate mm10? I'll put an alternative out there: DeepTools. [http://deeptools.readthedocs.io/en/latest/index.html][1] These guys did a fantastic job of coding up a suite of tools for assessing sequencing results. Most importantly ...
written 15 months ago by paul.e.gradie60
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Answer: A: Remove reads counts overlapping with blacklist regions in BAM files
... Good suggestions. Keep in mind - when you perform a cross strand correlation analysis to assess peak quality in your data, if you do not exclude blacklisted reads prior to this analysis (which generally uses aligned reads or bed converted intervals from these reads), then you will include these r ...
written 15 months ago by paul.e.gradie60
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Answer: A: Macs: Valueerror: Invalid Literal For Int() With Base 10: '1:N:0:'
... For anyone who is finding this far down the road (this post is 3.1 years old by now)... There is a decent chance that you may have the -f/--Format option set incorrectly. Make sure this agrees with the file type you are loading in for analysis. -f BAM or -f BED, etc. Cheers, Paul ...
written 15 months ago by paul.e.gradie60
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Answer: A: Data Normalization For Co-Expression Network Construction By Wgcna
... To bump an old question: Data normalization is handled internally within Cufflinks on a PER SAMPLE basis. For each transcriptome you assemble or quantify, calculation of the FPKM values include a normalization step using the DEseq geometric mean normalization method. If you want to compare across ...
written 20 months ago by paul.e.gradie60
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Comment: C: Comparing FPKM values from cufflinks and cuffnorm
... Thanks for your insights Devon - always find your thoughts useful here.  As a follow up to the FPKM comparison problem when you have different amounts of rRNA for example.. What if when you are running cufflinks to assemble your transcriptomes you use a rRNA, tRNA, and chrM mask file to mask these ...
written 21 months ago by paul.e.gradie60
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Comment: C: RNA-seq differential expression analysis, which aligner to choose between BWA/to
... Hi Brian,  I'm interested in using Seal, however I'm not sure where I would get a 'transcriptome.fa' file. Is that an output generated from BBmap?  On a side note - I'm extremely interested in your background; your training in computer science, your bioinformatics training and experience, how you ...
written 21 months ago by paul.e.gradie60

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