Package: fastamanager Version: 2.0.1-3 Architecture: all Maintainer: Olivier Langella Installed-Size: 229 Depends: openjdk-6-jre (>= 1.6), liblog4j1.2-java (>= 1.2.15), libcommons-httpclient-java (>= 3.1), libcommons-codec-java (>= 1.4), libcommons-logging-java (>= 1.1.1) Homepage: http://pappso.inra.fr/ Priority: optional Section: science Filename: pool/main/f/fastamanager/fastamanager_2.0.1-3_all.deb Size: 167104 SHA256: 4b75ba11f3a62546ce93e09629a7d2825a0ed6e36de79979dfde8206d9d00ca1 SHA1: 204afc4eafdba0f4b14ed870b71ac8c16018f64f MD5sum: d775d8aa066701fb706f62cf59e1f455 Description: helps to manage a Fasta file collection helps to manage a Fasta file collection Package: libquazip-doc Source: libquazip Version: 0.5.1-2~wheezy+1 Architecture: all Maintainer: Debian Med Packaging Team Installed-Size: 716 Multi-Arch: foreign Homepage: https://sourceforge.net/projects/quazip/ Priority: optional Section: doc Filename: pool/main/libq/libquazip/libquazip-doc_0.5.1-2~wheezy+1_all.deb Size: 202228 SHA256: f933f047edf1185d9a62a584bd611da32e0f1a85b7e1e7f0e97c6a6e350b7759 SHA1: 22dd8f365f8d2b8e68680e55e712896e4cd36af4 MD5sum: 57835efe72bf95b0926bcabce3f829f9 Description: C++ wrapper for ZIP/UNZIP (documentation) QuaZIP is a simple C++ wrapper over Gilles Vollant's ZIP/UNZIP package that can be used to access ZIP archives. It uses Trolltech's Qt toolkit. . QuaZIP allows you to access files inside ZIP archives using QIODevice API, and that means that you can also use QTextStream, QDataStream or whatever you would like to use on your zipped files. . QuaZIP provides complete abstraction of the ZIP/UNZIP API, for both reading from and writing to ZIP archives. . This package contains the API documentation in HTML. Package: live-build Version: 3.0.5-1~wheezy+1 Architecture: all Maintainer: Debian Live Project Installed-Size: 881 Depends: debootstrap | cdebootstrap | cdebootstrap-static Recommends: live-boot-doc, live-config-doc, live-manual-html | live-manual, cpio, gnu-fdisk Suggests: dosfstools, debian-keyring, xorriso, git, gpgv, loadlin, memtest86+ | memtest86, mtools, parted, squashfs-tools | mtd-tools, sudo | fakeroot, syslinux | grub, uuid-runtime, win32-loader Homepage: http://live.debian.net/devel/live-build/ Priority: optional Section: misc Filename: pool/main/l/live-build/live-build_3.0.5-1~wheezy+1_all.deb Size: 215348 SHA256: bf5b22ee074ec35e98df588ca6d2f02e8d542a8d680139f627447c2249845c0c SHA1: 92a7fdf22ac3004e0a0195a61d2e0a877ba7459d MD5sum: 563e9c11acc00ca52eaca2fe83996d63 Description: Live System Build Scripts live-build contains the scripts to build a live system from a configuration directory. Package: live-build-cgi Source: live-build Version: 3.0.5-1~wheezy+1 Architecture: all Maintainer: Debian Live Project Installed-Size: 123 Depends: live-build (= 3.0.5-1~wheezy+1) Recommends: apache2 | httpd, cron Homepage: http://live.debian.net/devel/live-build/ Priority: optional Section: misc Filename: pool/main/l/live-build/live-build-cgi_3.0.5-1~wheezy+1_all.deb Size: 77292 SHA256: cc07d7fafa6210200d97d871ad5d160ccdc21067adc78daea8d42d6484778407 SHA1: 84d8d29c4a01ed617e34e0a2b5d9c05843fbf306 MD5sum: 62ad7a1b26748132300544d690aa90b6 Description: Live System Build Scripts (CGI frontend) live-build contains the scripts to build a live system from a configuration directory. . This package contains the CGI frontend (experimental!). Package: masschroq Version: 2.1.0-4 Architecture: i386 Maintainer: Olivier Langella Installed-Size: 62 Depends: libc6 (>= 2.1.3), libgcc1 (>= 1:4.1.1), libqt4-network (>= 4:4.5.3), libqt4-xml (>= 4:4.5.3), libqt4-xmlpatterns (>= 4:4.5.3), libqtcore4 (>= 4:4.8.0), libqtgui4 (>= 4:4.5.3), libstdc++6 (>= 4.1.1), masschroq-common (= 2.1.0-4) Suggests: masschroq-doc, masschroq-gui, masschroq-studio Homepage: http://pappso.inra.fr/bioinfo/masschroq/ Priority: optional Section: science Filename: pool/main/m/masschroq/masschroq_2.1.0-4_i386.deb Size: 16794 SHA256: 8334da85e21636a8ab5a1337d74185982b515efd46ba7dcff47f0eeb9555c595 SHA1: 73dc504aa0a12f7b68eaf75e364655f04b4845e6 MD5sum: 162a9d71551c19ec79922d75938fa3c2 Description: Mass Chromatogram Quantification CLI (Command Line Interface) MassChroQ (Mass Chromatogram Quantification) software performs quantification of data obtained from LC-MS (Liquid Chromatography - Mass Spectrometry) techniques. In particular it performs : retention-time alignment of runs, XIC extraction and filtering, peak detection and quantification. Package: masschroq-common Source: masschroq Version: 2.1.0-4 Architecture: i386 Maintainer: Olivier Langella Installed-Size: 1005 Depends: libc6 (>= 2.1.3), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0), libqtcore4 (>= 4.6.3) Suggests: masschroq, masschroq-gui, masschroq-studio Conflicts: masschroq (<< 1.5.0) Replaces: masschroq (<< 1.5.0) Homepage: http://pappso.inra.fr/bioinfo/masschroq/ Priority: optional Section: science Filename: pool/main/m/masschroq/masschroq-common_2.1.0-4_i386.deb Size: 362510 SHA256: 4ecbe2e8572a41c1c4bd8c487c28d68c8b9156b1a1874ca4f7cc4221de5846c5 SHA1: 1c77b269369825fbc5d375f1df084ef89a409c80 MD5sum: 6e0b756a934e0ef5e5784d7a1ea1e0e1 Description: Mass Chromatogram Quantification shared libraries MassChroQ (Mass Chromatogram Quantification) software performs quantification of data obtained from LC-MS (Liquid Chromatography - Mass Spectrometry) techniques. In particular it performs : retention-time alignment of runs, XIC extraction and filtering, peak detection and quantification. Package: masschroq-condor Source: masschroq Version: 2.1.2-1 Architecture: all Maintainer: Olivier Langella Installed-Size: 39 Depends: masschroq, condor Suggests: masschroq-doc, masschroq-gui, masschroq-studio Homepage: http://pappso.inra.fr/bioinfo/masschroq/ Priority: optional Section: science Filename: pool/main/m/masschroq/masschroq-condor_2.1.2-1_all.deb Size: 7956 SHA256: ef70d035cb314f048064e4e63d3b7fd828ef18a028b7398633db2c031d738d63 SHA1: 351a9f3c473e962fc24a011edc634ca771463760 MD5sum: a388d2856be007047bea2c7b6c285ecc Description: Perl script to launch MassChroQ via condor job queue Perl script to launch MassChroQ via condor job queue Package: masschroq-doc Source: masschroq Version: 2.1.2-1 Architecture: all Maintainer: Olivier Langella Installed-Size: 534 Suggests: masschroq, masschroq-gui, masschroq-studio Homepage: http://pappso.inra.fr/bioinfo/masschroq/ Priority: optional Section: science Filename: pool/main/m/masschroq/masschroq-doc_2.1.2-1_all.deb Size: 517680 SHA256: 91577f6e5fc000a40d78f43468767c184b088e9bd8b3d7b5a81804b3102e5bb9 SHA1: 6e32d8f9c9128eff3c2fc87b03087dd353e715c4 MD5sum: 3d1c731cd072d368aeba6b1d01417811 Description: Mass Chromatogram Quantification documentation Installs PDF documentation for MassChroQ in /usr/share/doc/masschroq Package: masschroq-gui Source: masschroq Version: 2.1.0-4 Architecture: i386 Maintainer: Olivier Langella Installed-Size: 101 Depends: libc6 (>= 2.1.3), libgcc1 (>= 1:4.1.1), libqt4-network (>= 4:4.5.3), libqt4-xml (>= 4:4.5.3), libqt4-xmlpatterns (>= 4:4.5.3), libqtcore4 (>= 4:4.5.3), libqtgui4 (>= 4:4.5.3), libqwt5-qt4, libstdc++6 (>= 4.1.1), masschroq-common (= 2.1.0-4) Suggests: masschroq-doc, masschroq-studio Homepage: http://pappso.inra.fr/bioinfo/masschroq/ Priority: optional Section: science Filename: pool/main/m/masschroq/masschroq-gui_2.1.0-4_i386.deb Size: 32460 SHA256: 9627b4ab24dcb317fc2360c1c9562892caaad8473b74974717f1ed411d63348e SHA1: d7c9a584dde7bdb7ecae0c80be35525ecf4a759c MD5sum: 58bf606507d4845fa1622a6607b31dfb Description: Mass Chromatogram Quantification graphical user interface MassChroQ (Mass Chromatogram Quantification) software performs quantification of data obtained from LC-MS (Liquid Chromatography - Mass Spectrometry) techniques. In particular it performs : retention-time alignment of runs, XIC extraction and filtering, peak detection and quantification. Package: masschroq-studio Source: masschroq Version: 2.1.0-4 Architecture: i386 Maintainer: Olivier Langella Installed-Size: 391 Depends: libc6 (>= 2.1.3), libgcc1 (>= 1:4.1.1), libqt4-network (>= 4:4.5.3), libqt4-xml (>= 4:4.5.3), libqt4-xmlpatterns (>= 4:4.5.3), libqtcore4 (>= 4:4.6.1), libqtgui4 (>= 4:4.5.3), libqwt5-qt4 (>= 5.2.0), libstdc++6 (>= 4.6), masschroq-common (= 2.1.0-4) Suggests: masschroq-doc, masschroq-gui Homepage: http://pappso.inra.fr/bioinfo/masschroq/ Priority: optional Section: science Filename: pool/main/m/masschroq/masschroq-studio_2.1.0-4_i386.deb Size: 136060 SHA256: aee0ba0128ca7da2675ece23ea03fc8444b44c5eb6681a72a6bc0d9aaefd2b31 SHA1: 19be983b347216d802a5806f70df6a699c8e96a5 MD5sum: bb953f6a6450886117fd08feef4c8e85 Description: Mass Chromatogram Quantification graphical user interface to edit parameters MassChroQ (Mass Chromatogram Quantification) software performs quantification of data obtained from LC-MS (Liquid Chromatography - Mass Spectrometry) techniques. In particular it performs : retention-time alignment of runs, XIC extraction and filtering, peak detection and quantification. Package: mzmine Version: 2.12-2 Architecture: all Maintainer: Olivier Langella Installed-Size: 75177 Depends: openjdk-6-jre (>= 1.6) | openjdk-7-jre (>= 1.7), libjfreechart-java, r-cran-rjava, libjama-java, libgnujaf-java, libautomaton-java, libaxis-java, libbcprov-java, libantlr-java, libcommons-io-java, libcommons-logging-java, liblog4j1.2-java, libcommons-cli-java, libcommons-codec-java, libcommons-collections3-java, libcommons-compress-java, libcommons-discovery-java, libcommons-httpclient-java, libcommons-math-java, libjargs-java, cup, javahelp2, libjgrapht0.6-java, libjsr305-java, libmysql-java, libslf4j-java, libstax-java, libstax2-api-java, libvecmath-java, libwsdl4j-java, libxalan2-java, libxerces2-java, libxom-java, libxpp3-java Homepage: http://mzmine.sourceforge.net/ Priority: optional Section: science Filename: pool/main/m/mzmine/mzmine_2.12-2_all.deb Size: 70939638 SHA256: 7018bb73e9893a2a84ecf7f0e83677cb0ebf69c74abe9cce1719751ed1da3dc9 SHA1: 5baf4763dd31982658452fc2f619ec3633b5b356 MD5sum: ab22df80fa5542843c539d0d82689713 Description: mass-spectrometry data processing MZmine 2 is an open-source project delivering a software for mass-spectrometry data processing, with the main focus on LC-MS data. It is based on the original MZmine toolbox described in 2006 Bioinformatics publication, but has been completely redesigned and rewritten since then. Our main goal is to provide a user-friendly, flexible and easily extendable framework with a complete set of modules covering the entire LC-MS data analysis workflow. Package: pepnovo Version: 3.1.2010225-3 Architecture: i386 Maintainer: Olivier Langella Installed-Size: 20455 Depends: libc6 (>= 2.1.3), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0) Homepage: http://proteomics.ucsd.edu/Software/PepNovo.html Priority: optional Section: science Filename: pool/main/p/pepnovo/pepnovo_3.1.2010225-3_i386.deb Size: 6848604 SHA256: ace14f80b9dc0b5b3c35628bc4a25fff15dfa0cab6bd98ac3aba8f8b657e9880 SHA1: 386ecc86129d301a9e0c64561cca6f5f01f8190e MD5sum: c70d16b81729f53aedfcc5009d273711 Description: denovo protein identification denovo protein identification Original-Maintainer: Olivier Langella Package: r-cran-plotrix Version: 3.4-7-1~wheezy+1 Architecture: all Maintainer: Debian Science Team Installed-Size: 692 Depends: r-base-core (>= 3.0.1-3~wheezycran3.0) Homepage: http://cran.r-project.org/web/packages/plotrix/ Priority: optional Section: gnu-r Filename: pool/main/r/r-cran-plotrix/r-cran-plotrix_3.4-7-1~wheezy+1_all.deb Size: 599082 SHA256: a83a0edd6657a17772f7ab02aa9880c50c34b76ce807791b7f7e603cf6881bce SHA1: c42ae642e742d84c9b1d630243ea45b1feec66d4 MD5sum: c7fbe9fa999408965107122f20239a94 Description: GNU R package providing various plotting functions This R package provides lots of plots, various labeling, axis and color scaling functions. Some of them are: . arctext: Display text on a circular arc. barhier: Display a set of hierarchically associated variables barp: A bar plotting routine bin.wind.records: Classify wind direction and speed records. centipede.plot: Display a centipede plot clock24.plot: Plot values on a 24 hour "clockface". color.legend: Legend matching categories or values to colors dotplot.mtb: Minitab style dotplots. gantt.chart: Display a Gantt chart intersectDiagram: Display set intersections multhist: Plot a multiple histogram, as a barplot polar.plot: Plot values on a circular grid of 0 to 360 degrees. vectorField: Display magnitude/direction vectors weighted.hist: Display a weighted histogram . and many more. Read more about this package at http://cran.r-project.org/web/packages/plotrix/plotrix.pdf Package: tandem-mass Version: 1:2013.09.01-1~wheezy+1 Architecture: i386 Maintainer: The Debichem Group Installed-Size: 554 Depends: libc6 (>= 2.7), libexpat1 (>= 2.0.1), libgcc1 (>= 1:4.1.1), libstdc++6 (>= 4.4.0) Homepage: http://www.thegpm.org/TANDEM/ Priority: optional Section: science Filename: pool/main/t/tandem-mass/tandem-mass_2013.09.01-1~wheezy+1_i386.deb Size: 231814 SHA256: b9d8a34d542a39ec6c1159705ca0583059b82357e5bb0b89060ae618bafc439c SHA1: 13c3b288b52ff4e18fe5b0f806957ebda8d98e1c MD5sum: 85590495cf7cd7d321e12f91d5a11b12 Description: mass spectrometry software for protein identification X! Tandem can match tandem mass spectra with peptide sequences, in a process that is commonly used to perform protein identification. . This software has a very simple, unsophisticated application programming interface (API): it simply takes an XML file of instructions on its command line, and outputs the results into an XML file, which has been specified in the input XML file. The output file format is described at \fI`http://www.thegpm.org/docs/X_series_output_form.pdf'\fR. . Unlike some earlier generation search engines, all of the X! Series search engines calculate statistical confidence (expectation values) for all of the individual spectrum-to-sequence assignments. They also reassemble all of the peptide assignments in a data set onto the known protein sequences and assign the statistical confidence that this assembly and alignment is non-random. The formula for which can be found here. Therefore, separate assembly and statistical analysis software, e.g. PeptideProphet and ProteinProphet, do not need to be used. Package: task-pappso-desktop Version: 0.2 Architecture: all Maintainer: Olivier Langella Installed-Size: 27 Depends: cups, icedove, icedove-l10n-fr, iceweasel, iceweasel-l10n-fr, ttf-mscorefonts-installer, cups-pdf, software-center, libreoffice-l10n-fr (>= 4.1.4), libreoffice-help-fr (>= 4.1.4), libreoffice (>= 4.1.4), kde-runtime, libokularcore1, okular, phonon Homepage: http://pappso.inra.fr/bioinfo Priority: optional Section: misc Filename: pool/main/t/task-pappso-desktop/task-pappso-desktop_0.2_all.deb Size: 2322 SHA256: 625e3b5f2f82e8d18ae58880a289118c31aaee5157edc97beff9db59c5e2c779 SHA1: 2cb76fa65af0326cd457e2de5e5d8c8f34b03de3 MD5sum: be6d1d8afc5c62999ae9f750088b14be Description: minimum set of softwares for a desktop use minimum set of softwares for a desktop use in the PAPPSO team Package: task-pappso-tools Version: 0.3 Architecture: all Maintainer: Olivier Langella Installed-Size: 27 Depends: pwiz-tools, fastamanager, beads, masschroq-gui, masschroq-studio, masschroq-doc, xtandempipeline, openms, topp, grouping-protein, pepnovopipeline, denovopipeline-ng, xtandempipeline-doc, massxpert, mmass Homepage: http://pappso.inra.fr/bioinfo Priority: optional Section: misc Filename: pool/main/t/task-pappso-tools/task-pappso-tools_0.3_all.deb Size: 2330 SHA256: dfccbd272381f230a29850f6958d95cf1d564efcd027242d26874e2d9efbb5b9 SHA1: a490840d5d528aac044912371dfd00fe772f85b4 MD5sum: 53095ebca485c9ae209de0c522b12a65 Description: install proteomic software used on PAPPSO install proteomic software used on PAPPSO Package: xtandempipeline Version: 3.3.4-8 Architecture: all Maintainer: Olivier Langella Installed-Size: 3091 Depends: libswt-cairo-gtk-3-jni, icedtea-netx, openjdk-6-jre (>= 1.6) | openjdk-7-jre (>= 1.7), libswt-gtk-3.5-java | libswt-gtk-3.6-java | libswt-gtk-3-java, libbatik-java (>= 1.7), libswt-mozilla-gtk-3.5-jni | libswt-webkit-gtk-3.6-jni | libswt-webkit-gtk-3-jni, tandem-mass, liblog4j1.2-java (>= 1.2.15), libcommons-httpclient-java (>= 3.1), libcommons-codec-java (>= 1.4), libcommons-logging-java (>= 1.1.1) Conflicts: xtandem-cyclone, xtandemparser (<< 2.9.8-2~) Replaces: xtandemparser (<< 2.9.8-2~) Homepage: http://pappso.inra.fr/ Priority: optional Section: science Filename: pool/main/x/xtandempipeline/xtandempipeline_3.3.4-8_all.deb Size: 2734504 SHA256: 316e8755305f296a3cf1be550d1a681da37917d63f3718071ff7b0dea79e154e SHA1: b315de228f1d41e691e106264ee114e23b94d3b0 MD5sum: 3877bea94e028c765ec63421368527fc Description: loads and parses the xml results product by X!Tandem This Java application loads and parses the xml results product by X!Tandem, applies filters on E-value at peptide and protein levels, filters proteins on the basis of a minimum number of unique peptides, removes proteins specified in a contaminant database... Package: xtandempipeline-doc Source: xtandempipeline Version: 3.3.4-8 Architecture: all Maintainer: Olivier Langella Installed-Size: 2424 Suggests: xtandempipeline Homepage: http://pappso.inra.fr/ Priority: optional Section: science Filename: pool/main/x/xtandempipeline/xtandempipeline-doc_3.3.4-8_all.deb Size: 2454554 SHA256: 7226f012dfa089d9f4d4ab473b948f9372c68b6c25eee4d810468808580f3edf SHA1: 0ccd61595b4a6f44de80bd64cf5a874bdcf26151 MD5sum: c60de8e6dc09842576b8f93eb045dec6 Description: X!TandemPipeline documentation Installs PDF documentation for X!TandemPipeline in /usr/share/doc/xtandempipeline-doc