{"id":32563021,"url":"https://github.com/smithlabcode/preseqr","last_synced_at":"2025-10-29T02:56:16.662Z","repository":{"id":18022979,"uuid":"21054477","full_name":"smithlabcode/preseqR","owner":"smithlabcode","description":"An R package for estimating library complexity","archived":false,"fork":false,"pushed_at":"2022-09-04T19:54:39.000Z","size":1624,"stargazers_count":13,"open_issues_count":6,"forks_count":4,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-10-03T22:34:11.159Z","etag":null,"topics":["capture-recapture","library-complexity","r","r-package","sequencing","sequencing-coverage","sequencing-library"],"latest_commit_sha":null,"homepage":"","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/smithlabcode.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}},"created_at":"2014-06-20T22:33:31.000Z","updated_at":"2025-08-05T14:57:49.000Z","dependencies_parsed_at":"2022-09-15T03:30:56.418Z","dependency_job_id":null,"html_url":"https://github.com/smithlabcode/preseqR","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/smithlabcode/preseqR","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2FpreseqR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2FpreseqR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2FpreseqR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2FpreseqR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/smithlabcode","download_url":"https://codeload.github.com/smithlabcode/preseqR/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/smithlabcode%2FpreseqR/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":281549786,"owners_count":26520515,"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","status":"online","status_checked_at":"2025-10-29T02:00:06.901Z","response_time":59,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":["capture-recapture","library-complexity","r","r-package","sequencing","sequencing-coverage","sequencing-library"],"created_at":"2025-10-29T02:56:07.868Z","updated_at":"2025-10-29T02:56:16.654Z","avatar_url":"https://github.com/smithlabcode.png","language":"R","readme":"preseqR\n=======\n\nCode in this repository aims to expand the functionality of Preseq and\nmake it available in the R statistical computing enviroment. There are\nfive ways this is supposed to work:\n\n1.  The basic functionality of the `preseq` program, initially\n    focusing only on library complexity, is available. These functions\n    contain the string \"rfa\" as part of their names.\n\n2.  The mathematical routines for doing rational function\n    approximation via continued fractions were implemented as a\n    wrapper for existing functionality in C++. This changed since\n    version 3.1.1, and now all functionality is in R.\n\n3.  Fitting a zero-truncated negative binomial distribution to the\n    sample is available. These functions include the string \"ztnb\" as\n    part of the names.\n\n4.  The simulation module is used to generate samples based on mixture\n    of Poisson.\n\n5.  Extra functions are provided to estimate the number of species\n    represented at least r times in a random sample.\n\nSee the [preseqR](https://cran.r-project.org/package=preseqR) package\non CRAN for details\n\nUPDATE HISTORY\n==============\n\nUpdates in version 4.0.0\n------------------------\n1. Improve the user interface for core functions\n2. Add functions to optimize the depth of single-cell whole-genome\n   sequencing experiments and whole-exome sequencing experiments\n3. Add functions to predict the sample coverage, which is the\n   probability of sampling an observed species from a population\n4. Add functions to predict the fraction of k-mers represented at\n   least r times in a sequencing experiment\n\nUpdates in version 3.1.2\n------------------------\n1. Fixed a bug for removing defects\n\nUpdates in version 3.1.1\n------------------------\n1. Substituted embedded C++ code with R code\n2. Removed the dependencies on the software preseq\n\nUpdates in version 3.0.1\n------------------------\n1. Fixed a bug in Chao's estimator\n2. Fixed issues for a Solaris C++ compiler.\n\nUpdates in version 3.0.0\n------------------------\n1. We have changed the return types of many functions in the\n   package. These functions no longer generate estimated accumulative\n   curves.  Instead, they return function types, which are estimators\n   for the number of species represented by at least r indivdiduals in\n   a random sample.\n2. We added several estimators for predicting the number of species\n   represented by at least r individuals in a random sample\n\nUpdates in version 2.1.1\n========================\n\nWe have changed the interfaces for most of our exported functions. We\nadd new estimators for the number of species represented by at least r\nindividuals in a random sample.\n\nINSTALLATION\n============\n\n1. We recommand everyone to install the package `preseqR` from CRAN.\n   It can be easily done by in an R session by typing:\n   ```R\n   \u003einstall.packages(\"preseqR\")\n   ```\n\n2. The following instructions are for installing the package from the\n   source. Assume the source code of `preseqR` has been pulled from the\n   git repo and it is under the current directory. Start a session in an\n   R interpreter and type:\n   ```R\n   \u003einstall.packages(\"polynom\")\n   \u003einstall.packages(\"preseqR\", repos=NULL, type=\"source\")\n   ```\n   Note that the package `polynom` is required by `preseqR`.\n\nCONTACTS AND BUG REPORTS\n========================\n\nAndrew D. Smith\nandrewds@usc.edu\n\nCOPYRIGHT AND LICENSE INFORMATION\n=================================\n\nCopyright (C) 2017-2022 Chao Deng and Andrew D. Smith\n\nAuthors: Chao Deng and Andrew D. Smith\n\nThis is free software: you can redistribute it and/or modify it under\nthe terms of the GNU General Public License as published by the Free\nSoftware Foundation, either version 3 of the License, or (at your\noption) any later version.\n\nThis software is distributed in the hope that it will be useful, but\nWITHOUT ANY WARRANTY; without even the implied warranty of\nMERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU\nGeneral Public License for more details.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmithlabcode%2Fpreseqr","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsmithlabcode%2Fpreseqr","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsmithlabcode%2Fpreseqr/lists"}