https://github.com/wlandau/fbseqcomputation
https://github.com/wlandau/fbseqcomputation
Last synced: about 1 month ago
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- Host: GitHub
- URL: https://github.com/wlandau/fbseqcomputation
- Owner: wlandau
- Created: 2016-02-25T04:22:46.000Z (about 9 years ago)
- Default Branch: main
- Last Pushed: 2020-10-27T16:20:20.000Z (over 4 years ago)
- Last Synced: 2025-02-14T12:40:44.936Z (3 months ago)
- Language: R
- Size: 33.2 KB
- Stars: 0
- Watchers: 5
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
[](https://zenodo.org/badge/latestdoi/22809/wlandau/fbseqComputation)
# fbseqComputation
[`fbseqComputation` package](https://github.com/wlandau/fbseqComputation) is a smaller version of the [`fbseqStudies` package](https://github.com/wlandau/fbseqStudies) package, created becase [`fbseqStudies` package](https://github.com/wlandau/fbseqStudies) reveals too much too soon. [`fbseqComputation` package](https://github.com/wlandau/fbseqComputation) 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](https://github.com/wlandau/fbseq) and [`fbseqCUDA` package](https://github.com/wlandau/fbseqCUDA) 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](https://github.com/wlandau/fbseqComputation/blob/master/DESCRIPTION) file.
- A [CUDA](http://www.nvidia.com/object/cuda_home_new.html)-capable [NVIDIA graphics processing unit (GPU)](https://developer.nvidia.com/cuda-gpus) with compute capability 2.0 or greater. More information about CUDA is available through [NVIDIA](http://www.nvidia.com/).
- [CUDA](http://www.nvidia.com/object/cuda_home_new.html) 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](https://github.com/wlandau/fbseqComputation/releases) on the project's [GitHub page](https://github.com/wlandau/fbseqComputation). 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 [email protected]:wlandau/fbseqComputation.git
R CMD build fbseqComputation
R CMD INSTALL ...
```
where `...` is replaced by the name of the tarball produced by `R CMD build`.