This is the PDF of the GenABEL tutorial, a book on how to use the GenABEL package and several other tools from the GenABEL suite (see. for the GenABEL project contributors. [ @GenAproj | www. . posts on forum. Open-source tutorial. GenABEL package. GenABEL suite. PredictA. PredictA. GenABEL tutorial. GenABEL tutorial Street, Suite , Mountain View, California, , USA. >= library(GenABEL) data( srdta) @.
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Open source, Scientific software, Software development, Community building, Statistical genetics, Genomics, Statistical methodology. Ten simple rules for a successful cross-disciplinary collaboration. In we have started to use tuutorial Jenkins Continuous Integration server.
The GenABEL Tutorial | Zenodo
Usage statistics such as number of visits and country of origin of visitors are monitored using Google Analytics http: The big challenges of big data. However, the 11 packages presented in this paper have been published previously in tutorkal shape or form, albeit presumably not in their most recent version.
The project has benefited from an open development model, facilitating communication and code sharing between the parties involved. Furthermore, our open development process has resulted in transparent development of methods and software, including public code thtorial, a large fraction of bugs being submitted by members of the community, and quick incorporation of bug fixes.
The GenABEL Tutorial
I have read this submission. It enables a free flow of information between the layers in the project resulting in rapid feedback between the various levels.
The original publication of tutoril GenABEL package for statistical analysis of genotype data 10 has led to the evolution of ttorial community which we now call the GenABEL project, which brings together scientists, software developers and end users with the central goal of making statistical thtorial work by openly developing and subsequently implementing statistical models into user-friendly software.
Interactive user support is mostly done through our forum http: Increasing the power of genome wide association studies in natural populations using repeated measures-evaluation and implementation. Currently, the suite consists of 11 officially released tools cf. Moreover, our experience shows that once the peer-reviewed article describing a tool has been published, funding and time to tjtorial development and support of that tool are usually limited or non-existent, and consequently, the tool often slowly fades into oblivion.
It is my understanding that the manuscript is aimed at reaching potential new users, but even to old users, unaware of the possible new tools included in the GenABEL project.
Furthermore, having an active forum where users can help each other allows the developers to focus on fixing bugs and implementing new features. Once the paper describing the tool has been published, the tool is no longer developed further and is left to its own device.
Moreover, compared to having individual users e-mailing a package author, who may be on holiday or otherwise unavailable, an open forum where users and developers collaborate helps in geanbel the time-to-answer. Nevertheless, despite limited amount of novel scientific ideas or scientific results in the current manuscript, the authors have clearly put a lot of work into creating a very impressive interactive user and developer community.
Collaborative software development using R-forge.
The GenABEL Tutorial
The field of statistical gen- omics lies at the heart of current research into the genetic aetiology of human disease and personalized or precision medicine 1. Interaction with the user community is done via social media like Twitter https: Development infrastructure The GenABEL project welcomes contributions of all sorts, from new tools to fixing spelling errors in the documentation, to bug reports and feature requests.
Region-based association analysis of human quantitative traits in related individuals. First of all it is a central, easy to point to reference. Torvalds L, Diamond D: An R package “VariABEL” titorial genome-wide searching of potentially interacting loci by testing genotypic variance heterogeneity.
Table 1 and two that are in beta stage. A multi-language computing environment for literate programming and reproducible research. Best practices for scientific computing. Aulchenko b, 1, 3, 4, 5. J Am Med Inform Assoc. Interaction with the user community The GenABEL project website is the central tugorial that points to package descriptions, tutorials, the development website, and other information for potential and existing users and developers.
Most scientific software is written by only a few authors, often a student working on a thesis. The total number of visits in that period wasof which came from unknown cities.
It includes functions to compute univariate and multivariate odds ratios of the predictors, the area under the receiver operating characteristic ROC curve AUCHosmer-Lemeshow goodness of fit test, reclassification table, net reclassification improvement and integrated discrimination improvement GWAS usually involves meta-analysis of the regression results of various cohorts.
Therefore, the community has the option to mark a tool as obsolete, warning the user that bugs will no longer be fixed and support is limited or non-existent. As an example of the information that can be obtained from this data, Figure 2 shows the top 20 cities of origin of the visitors of the GenABEL website in the period of 28 April till 28 April Moreover, public access to the source code is an important ingredient for active participation by people from outside the core development team and is paramount for reproducible research.
The GenABEL project welcomes contributions of all sorts, from new tools to fixing spelling errors in the documentation, to bug reports and feature requests.
The first hurdle many users of scientific software encounter is the installation process. A web forum is used to channel user questions and discussions, further promoting the use of the GenABEL suite.
Development and application of genomic control methods for tutorila association studies using non-additive models. This article has been cited genaebl other articles in PMC.
Open in a separate window. Journal List FRes v. Lastly, to reiterate, the GenABEL is a very impressive large scale project that is heavily used by the community! National Center for Biotechnology InformationU. Support Center Support Center. It is the second tutoorial tool from the suite with more than citations according to Google Scholar