Blog Archives

DNA methylation (RRBS or target capture) analysis with R

February 20, 2012
By

Reduced Representation Bisulfite sequencing (RRBS) is a popular technique for measuring methylation levels across genome. Although it does not have the full genome coverage, it covers many important regions for methylation. Below, I shared a tutorial a...

Read more »

methylKit: R package for DNA methylation analysis

December 21, 2011
By

High-throughput bisulfite sequencing based methods are popular for measuring genome-wide DNA methylation levels. Here is an R package that helps with the analysis of such DNA methylation data. Although, it is still under heavy development current funct...

Read more »

knitr: nice alternative for Sweave

December 17, 2011
By

I recently discovered knitr for dynamic report generation in R. It seems like a very powerful alternative to Sweave. Particularly, I am interested in png graphic device support (it supports more than 20 graphic devices) and R code formatting.Check it o...

Read more »

Fast(ish) extraction of exon locations from a BED12 file using data.table

March 20, 2011
By

Here is a fast R function to extract exon locations from a BED12 file. Note that fast is a relative term, the function below is fast enough for me, may not be fast enough for others :) Anyway, a BED12 file typically has locations of genomic features (t...

Read more »

Fast(ish) extraction of exon locations from a BED12 file using data.table

March 20, 2011
By

Here is a fast R function to extract exon locations from a BED12 file. Note that fast is a relative term, the function below is fast enough for me, may not be fast enough for others :) Anyway, a BED12 file typically has locations of genomic features (t...

Read more »

Applying functions on groups: sqldf, plyr, doBy, aggregate or data.table ?

March 17, 2011
By
Applying functions on groups: sqldf, plyr, doBy, aggregate or data.table ?

Which one of the sqldf, plyr, doBy and aggregate functions/packages would be faster for applying functions on groups of rows? I was wondering about this earlier in this post.  It seems sqldf would be the fastest according to a post in manipulatr m...

Read more »

Applying functions on groups: sqldf, plyr, doBy, aggregate or data.table ?

March 17, 2011
By
Applying functions on groups: sqldf, plyr, doBy, aggregate or data.table ?

Which one of the sqldf, plyr, doBy and aggregate functions/packages would be faster for applying functions on groups of rows? I was wondering about this earlier in this post.  It seems sqldf would be the fastest according to a post in manipulatr m...

Read more »

Tips on installing R extension for Rapidminer on Mac OS X

March 9, 2011
By
Tips on installing R extension for Rapidminer on Mac OS X

Rapidminer is a cool toy to play with machine-learning/data-mining algorithms and it can interface with R. However, it was a bit problematic for me to get the R extension working properly on Mac OS X Leopard for R 2.11. Here is what works for me at the...

Read more »

Tips on installing R extension for Rapidminer on Mac OS X

March 9, 2011
By
Tips on installing R extension for Rapidminer on Mac OS X

Rapidminer is a cool toy to play with machine-learning/data-mining algorithms and it can interface with R. However, it was a bit problematic for me to get the R extension working properly on Mac OS X Leopard for R 2.11. Here is what works for me at the...

Read more »

Calling BEDtools from R

February 22, 2011
By

BEDtools suite provides command-line functionality when dealing with genomic coordinate based operations, such as overlapping bed files or getting coverage of a bed file over a genome (similar, not exactly same, functionality in R is provided by IRange...

Read more »

Sponsors

Mango solutions



RStudio homepage



Zero Inflated Models and Generalized Linear Mixed Models with R

Quantide: statistical consulting and training



http://www.eoda.de







ODSC

ODSC

CRC R books series





Six Sigma Online Training





Contact us if you wish to help support R-bloggers, and place your banner here.

Never miss an update!
Subscribe to R-bloggers to receive
e-mails with the latest R posts.
(You will not see this message again.)

Click here to close (This popup will not appear again)