{"id":16273727,"url":"https://github.com/wlandau/fbseqcomputation","last_synced_at":"2025-04-08T16:12:53.029Z","repository":{"id":72824994,"uuid":"52496495","full_name":"wlandau/fbseqComputation","owner":"wlandau","description":null,"archived":false,"fork":false,"pushed_at":"2020-10-27T16:20:20.000Z","size":34,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":5,"default_branch":"main","last_synced_at":"2025-02-14T12:40:44.936Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/wlandau.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2016-02-25T04:22:46.000Z","updated_at":"2016-04-05T15:39:01.000Z","dependencies_parsed_at":null,"dependency_job_id":"55eab09e-dd1c-4f40-b1a2-ce9d82234b2e","html_url":"https://github.com/wlandau/fbseqComputation","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/wlandau%2FfbseqComputation","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/wlandau%2FfbseqComputation/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/wlandau%2FfbseqComputation/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/wlandau%2FfbseqComputation/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/wlandau","download_url":"https://codeload.github.com/wlandau/fbseqComputation/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247878021,"owners_count":21011158,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-10-10T18:25:29.511Z","updated_at":"2025-04-08T16:12:53.025Z","avatar_url":"https://github.com/wlandau.png","language":"R","readme":"[![DOI](https://zenodo.org/badge/22809/wlandau/fbseqComputation.svg)](https://zenodo.org/badge/latestdoi/22809/wlandau/fbseqComputation)\n\n# fbseqComputation\n\n[`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.\n\n# System requirements\n\n- 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.\n- 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/).\n- [CUDA](http://www.nvidia.com/object/cuda_home_new.html) version 6.0 or greater.\n- 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.\n\n# Installation\n\n## Option 1: install a stable release (recommended).\n\nNavigate 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.\n\n## Option 2: use `install_github` to install the development version.\n\nFor this option, you need the `devtools` package, available from CRAN or GitHub. Open R and run \n\n```{r, eval=F}\nlibrary(devtools)\ninstall_github(\"wlandau/fbseqComputation\")\n```\n\n## Option 3: build the development version from the source.\n\nOpen a command line program such as Terminal in Mac/Linux and enter the following commands.\n\n```\ngit clone git@github.com:wlandau/fbseqComputation.git\nR CMD build fbseqComputation\nR CMD INSTALL ...\n```\n\nwhere `...` is replaced by the name of the tarball produced by `R CMD build`. ","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwlandau%2Ffbseqcomputation","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fwlandau%2Ffbseqcomputation","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fwlandau%2Ffbseqcomputation/lists"}