README.md

In wlandau/fbseqComputation: fbseqComputation

fbseqComputation

fbseqComputation package is a smaller version of the fbseqStudies package package, created becase fbseqStudies package reveals too much too soon. fbseqComputation package reproduces the results of Section 5 ("Assessing computational tractability") of a paper entitled "A fully Bayesian strategy for high-dimensional hierarchical modeling using massively parallel computing" by Will Landau and Dr. Jarad Niemi. The goal is to assess the computational tractability of fbseq package and fbseqCUDA package using a real RNA-seq dataset and a simulation study based off this dataset. See the original paper for details.

System requirements

• The R version and R packages listed in the "Depends", "Imports", and "Suggests" fields of the "package's DESCRIPTION file.
• A CUDA-capable NVIDIA graphics processing unit (GPU) with compute capability 2.0 or greater. More information about CUDA is available through NVIDIA.
• CUDA version 6.0 or greater.
• Optional: the code uses double precision values for computation, so GPUs that natively support double precision will be much faster than ones that do not.

Installation

Option 1: install a stable release (recommended).

Navigate to a list of stable releases on the project's GitHub page. Download the desired tar.gz bundle, then install it either with install.packages(..., repos = NULL, type="source") from within R R CMD INSTALL from the Unix/Linux command line.

Option 2: use install_github to install the development version.

For this option, you need the devtools package, available from CRAN or GitHub. Open R and run

```{r, eval=F} library(devtools) install_github("wlandau/fbseqComputation")

## Option 3: build the development version from the source.

Open a command line program such as Terminal in Mac/Linux and enter the following commands.

git clone [e-mail]:wlandau/fbseqComputation.git R CMD build fbseqComputation R CMD INSTALL ... ```

where ... is replaced by the name of the tarball produced by R CMD build.

wlandau/fbseqComputation documentation built on May 4, 2019, 8:43 a.m.