Bug#819355: ITP: augustus -- gene prediction in eukaryotic genomes
Package: wnpp Severity: wishlist Owner: Sascha Steinbiss * Package name: augustus Version : 3.2.1 Upstream Author : Lizzy Gerischer, Oliver Keller, Stefanie König, Lars Romoth, Mario Stanke * URL : http://bioinf.uni-greifswald.de/augustus/ * License : Artistic Programming Lang: C++ Description : gene prediction in eukaryotic genomes AUGUSTUS is a software for gene prediction in eukaryotic genomic sequences that is based on a generalized hidden Markov model, which is a probabilistic model of a sequence and its gene structure. After learning gene structures from a reference annotation, AUGUSTUS uses the HMM to recognize genes in a new sequence and annotates it with the regions of identified genes. External hints, e.g. from RNA sequencing, EST or protein alignments etc. can be used to guide and improve the gene finding process. The result is the set of most likely gene structures that comply with all given user constraints, if such gene structures exist. AUGUSTUS already includes prebuilt HMMs for many species, as well as scripts to train custom models using annotated genomes. This package will be maintained under the umbrella of the Debian Med Packaging Team.
Bug#819363: ITP: r-cran-shiny -- GNU R web application framework
Package: wnpp Severity: wishlist Owner: Andreas Tille * Package name: r-cran-shiny Version : 0.13.1 Upstream Author : Winston Chang and others * URL : https://cran.r-project.org/web/packages/shiny/ * License : MIT Programming Lang: GNU R Description : GNU R web application framework Makes it incredibly easy to build interactive web applications with R. Automatic "reactive" binding between inputs and outputs and extensive pre-built widgets make it possible to build beautiful, responsive, and powerful applications with minimal effort. Remark: This package is part of a pyramid of dependencies required for the final target r-cran-treescape and will be maintained by the Debian Med team at https://anonscm.debian.org/git/debian-med/r-cran-shiny.git
Bug#819389: ITP: r-cran-bh -- GNU R package with Boost headers
Package: wnpp Owner: Dirk Eddelbuettel Severity: wishlist * Package name: r-cran-bh Version : 1.60.0-1-1 Upstream Author : Jay Emerson and Dirk Eddelbuettel * URL or Web page : http://cloud.r-project.org/package=BH * License : BSL-1.0 Description : GNU R package with Boost header This package (for which I upstream as well) has become a build dependency for a number of CRAN packages, and hence Andreas Tille asked me to package this. There is of course overlap with liboost-all-dev and its components. BH is however very useful in the R and CRAN world as it provides a uniform layer of Boost headers there (with minimal patching; I have to shorten one path name). So in the interest of having Debian behave like other systems it makes sense to package it here. We are also currently ahead of Debian packaging which is still at Boost 1.58.0. Regards, Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org
Bug#819392: ITP: geg -- GTK+ Equation Grapher
Package: wnpp Severity: wishlist Owner: Georges Khaznadar * Package name: geg Version : 2.0.2 Upstream Authors: 1998 David Bryant 2009-2015 Barry deFreese 2016 Jean-Pierre Demailly * URL : https://sourceforge.net/projects/sf- xpaint/files/geg/geg-2.0.2.tar.bz2/download * License : GPL Programming Lang: C Description : GTK+ Equation Grapher geg is a very simple utility for parsing and plotting 2D-functions, eg f(x) = 3 + sin(x), and much more complicated functions of course. It is written with GTK+ and provides a neat, configurable user interface. geg is not the only package usable to plot 2d functions, but it is simpler to use, and very lightweight: it can be preferred for low-end machines, and in any case when simplicity of use is the main constraint. This package has been part of Debian woody, and removed in year 2009 due to lack of maintenance, see https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=515284 Now it is maintained upstream by Jean-Pierre Demailly who is a reliable friend, and I shall make all updates when necessary. This package is now in a stable state.
