RPHAST is an R interface to the PHAST software package. It contains much of the functionality of phast within a highly-developed statistical programming environment, and is easy and fun to use.
To install the latest version of the package directly from github using the devtools package, use the command in R:
devtools::install_github("CshlSiepelLab/RPHAST")
The RPHAST package source code can be downloaded here - rphast_1.6.11.tar.gz
RPHAST can be installed from source code using the command in R:
install.packages("rphast_1.6.11.tar.gz", repos=NULL, type="source")
The package source can also be installed from the command line on non-Windows platforms using the command:
R CMD INSTALL rphast_1.6.tar.gz
*NOTE: If you do not have administrator privileges, you may need to specify a directory where the package will be stored. This can be done with the "library" argument to install.packages, or by using R CMD INSTALL --library=/path/to/library on the command line.
| Sweave Source | Description | |
|---|---|---|
| Vignette1.pdf | Vignette1.Rnw | Read in alignment and features, estimate neutral model based on 4d sites using phyloFit, run phyloP and phastCons |
| Vignette2.pdf | Vignette2.Rnw | Detect rodent-accelerated regions using a multiple species alignment of human chromosome 22, assess significance by simulation |
| Vignette3.pdf | Vignette3.Rnw | Create custom phylogenetic HMM which models a transcription factor binding site; verify the model on a simulated alignment |
| Vignette4.pdf | Vignette4.Rnw | Introduction to detecting GC-biased gene conversion with RPHAST; nucleotide and phylo-HMM models |
| RPHAST-Manual.pdf | RPHAST Reference Manual |
Problems, questions, feature requests should be directed to phasthelp@cshl.edu.