[R-bloggers] 10 R packages every data scientist should know about (and 6 more aRticles)

Do you have R packages pertaining to genomics that you might feel should make it to a 'Top 10 R packages for Bioinformatics' ? 

The yhat blog lists 10 R packages they wish they'd known about earlier. Drew Conway calls them "10 reasons to always start your analysis in R". They're all very useful R packages that every data scientist should be aware of. They are:

1. sqldf (for selecting from data frames using SQL)
2. forecast (for easy forecasting of time series)
3. plyr (data aggregation)
4. stringr (string manipulation)
5. Database connection packages RPostgreSQL, RMYSQL, RMongo, RODBC, RSQLite
6. lubridate (time and date manipulation)
7. ggplot2 (data visulization)
8. qcc (statistical quality control and QC charts)
9. reshape2 (data restructuring)
10. randomForest (random forest predictive models)

You can find links to all of these packages and tips on how to use them at link below.

yhat blog: 10 R packages I wish I knew about earlier

Saw figure 2 from this paper from Stephan Schuster in talks wayyy back and his point about using different platforms/chemistry to reduce bias was always in the back of my head when handling single platform data.

Great work getting this finally published. 

His criteria for variant calling should be also a good starting reference point. 

"We used SAMtools version 0.1.16 to call the variants in the Illumina reads. We required a minimum coverage of 4, a maximum coverage of 60 and a minimum quality of 20 for the SNPs and indels that were found to be on the autosomes. We reduced the maximum coverage requirement to 45 for the sex chromosomes and increased it to 10,000 for the mitochondrial DNA. Only homozygous SNP and indels calls were kept from the sex chromosomes and mtDNA."

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0055089

PLoS One. 2013;8(2):e55089. doi: 10.1371/journal.pone.0055089. Epub 2013 Feb 6.

Comparison of sequencing platforms for single nucleotide variant calls in a human sample.

Ratan A, Miller W, Guillory J, Stinson J, Seshagiri S, Schuster SC.

Source

Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, Pennsylvania, United States of America.

Abstract

Next-generation sequencings platforms coupled with advanced bioinformatic tools enable re-sequencing of the human genome at high-speed and large cost savings. We compare sequencing platforms from Roche/454(GS FLX), Illumina/HiSeq (HiSeq 2000), and Life Technologies/SOLiD (SOLiD 3 ECC) for their ability to identify single nucleotide substitutions in whole genome sequences from the same human sample. We report on significant GC-related bias observed in the data sequenced on Illumina and SOLiD platforms. The differences in the variant calls were investigated with regards to coverage, and sequencing error. Some of the variants called by only one or two of the platforms were experimentally tested using mass spectrometry; a method that is independent of DNA sequencing. We establish several causes why variants remained unreported, specific to each platform. We report the indel called using the three sequencing technologies and from the obtained results we conclude that sequencing human genomes with more than a single platform and multiple libraries is beneficial when high level of accuracy is required.

PMID:

 

23405114

 

[PubMed - in process]

Article: FedEx's file-transfer capacity versus the Internet

Ever considered FedEx maximum bandwidth ? Lazy to do the math? It's in here. 

Though I wonder having all the data split across HDDs really count since u can't possibly access all the data at once. 

FedEx's file-transfer capacity versus the Internet
http://boingboing.net/2013/02/05/fedexs-file-transfer-capacit.html

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Article: Source Code for Biology and Medicine | Abstract | CrypticIBDcheck: an R package for checking cryptic relatedness in nominally unrelated individuals

Source Code for Biology and Medicine | Abstract | CrypticIBDcheck: an R package for checking cryptic relatedness in nominally unrelated individuals
http://www.scfbm.org/content/8/1/5/abstract

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Fwd: Save 15% on a New MiSeq System – Limited-Time Offer

Ask for your discount!

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From: "Illumina" <Community@illumina.com>
Date: 6 February, 2013 5:35:59 AM GMT+08:00
To: 
Subject: Save 15% on a New MiSeq System – Limited-Time Offer
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Get It Now   www.illumina.com     Dear Valued Researcher, If you are ready to experience the power of MiSeq, the most accurate and easiest-to-use benchtop sequencer—why not save a little money on the way? Now through March 31, 2013, purchase at least 15 MiSeq Sequencing Reagent Kits at list price and receive 15% off your MiSeq System. Next-generation sequencing doesn't get any easier than this. Take advantage of this offer and get started today.   *Offer not valid with other discounts and promotions. Eligible kits are MiSeq Reagent Kits v2 (50-, 300- and 500-cycles), catalog numbers: MS-102-2001, MS-102-2002, and MS-102-2003.     Sent by Illumina  |  5200 Illumina Way  |   San Diego, CA, 92122 www.illumina.com  |  Unsubscribe |  Update Profile

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Handling R packages Feb 2013 issue Linux Journal

The kind folks at http://www.linuxjournal.com/ have provided me an 2013 Feb issue. Can't tell you how much of Linux I have picked up from there with its easy prose and graphical howtos. In the Feb 2013 issue, they have focused on the theme sys admin. Definitely useful things inside for the starting bioinformatician who wishes to dabble with working directly off a *nix machine :)

Other topics in this issue includes

In the February 2013 issue:

• Manage Your Virtual Deployment with ConVirt
• Use Fabric for Sysadmin Tasks on Remote Machines
• Spin up Linux VMs on Azure
• Make Your Android Device Play with Your Linux Box
• Create a Colocated Server with Raspberry Pi

You can check out a preview of the contents here

February 2013 Issue of Linux Journal: System Administration

By Shawn Powers | Feb 01, 2013

Fwd: [BioRuby] Genomer: a ruby project to simplify genome finishing

Looks intriguing! anyone else using it? 

---------- Forwarded message ----------
From: Michael Barton <mail AT michaelbarton.me.uk>
Date: Sun, Feb 3, 2013 at 5:34 AM
Subject: [BioRuby] Genomer: a ruby project to simplify genome finishing
To: BioRuby Mailing List


Hi Everyone,

I've been working a sequencing microbial genomes during my current post doc
position. I've combined many of the ruby scripts I was using into a single tool
called "genomer" which might be of interest to other bioinformaticians working
in the same area.

I used this tool to simplify the smaller, mundane tasks associated with a
genome. For instance moving contigs and associated annotations around,
generating the required files to submit to GenBank, and generating summaries of
the genome scaffold.

I created a small screencast for anyone who is interested in finding out more:
http://youtu.be/HfsdJOELFjs?hd=1

I wrote this tool to satisfy my own needs and use genomer extensively for the
microbial genome projects in our lab. My GNU Makefile (http://bit.ly/WMKlCZ)
from a P. fluorescens project illustrates how genomer combined with GenBank's
tbl2asn can be used to build the all files required for genome submission.

Hopefully genomer may be useful to other bioinformaticians and simplify the
steps required to finish and submit a genome.

Thanks

Michael Barton

_______________________________________________
BioRuby Project - http://www.bioruby.org/
http://lists.open-bio.org/mailman/listinfo/bioruby

I have created an additional screencast to follow up. This provides a more
concrete example of using genomer to generate the files required to submit a
genome project to GenBank.

http://www.youtube.com/watch?v=jVn62pMnIRA&hd=1

Thanks

Mike