[{"_1":2,"_161":-5,"_162":-5},"loaderData",{"_3":4,"_17":18,"_25":26,"_140":141},"root",{"_5":-5,"_6":-7,"_7":8,"_9":-7,"_10":11,"_12":-7,"_13":14,"_15":16},"currentUser","primaryEmail","siteVerification","6LeIxAcTAAAAAJcZVRqyHh71UMIEGNQ_MXjiZKhI","toast","enableDev",false,"incidentStatus","theme","system","contrast","normal","routes/_layout",{"_19":-5,"_20":21,"_22":21,"_23":11,"_24":21},"username","isAskGordonEnabled",true,"isUsingNewTemplate","showMinimalLanding","showHoneypotTrap","routes/_layout.r.$namespace.$reponame",{"_27":28,"_29":-5,"_30":11,"_31":11,"_32":33,"_34":35,"_36":-5,"_37":11,"_38":39,"_88":-5,"_89":90,"_129":-5,"_130":11,"_131":21,"_132":11,"_133":-5,"_134":11,"_135":-5,"_136":137,"_138":91,"_139":-7},"canonicalUrl","https://hub.docker.com/r/cpanse/rawdiag/tags","mcpServer","canSeeDockerfile","canSeeAutobuilds","namespace","cpanse","reponame","rawdiag","cloudBuildSource","isAutobuildsAvailable","repo",{"_40":41,"_42":43,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":55,"_57":35,"_32":33,"_58":59,"_60":44,"_61":62,"_63":62,"_64":65,"_66":-5,"_67":68,"_69":70,"_71":11,"_72":33,"_73":74,"_79":21,"_80":81,"_85":33,"_86":87},"categories",[],"content_types",[44],"image","date_registered","2018-06-12T10:33:47.290341Z","description","docker image to fire up shiny application","is_private","last_updated","2018-08-21T12:42:58.80349Z","last_modified","2024-10-16T13:48:34.145251Z","media_types",[56],"application/vnd.docker.container.image.v1+json","name","pull_count",1100,"repository_type","star_count",1,"status","status_description","active","source","collaborator_count",0,"full_description","# rawDiag

\n\n\n\n\nan R package supporting rational LC-MS method optimization for bottom-up proteomics on multiple OS platforms\n\n\nmain features:\n \n1. **multiplatform** and **fast** reading through using [The New RawFileReader from Thermo Fisher Scientific](http://planetorbitrap.com/rawfilereader).\n2. uses latest visualization generation through using Rs [ggplot2](https://cran.r-project.org/package=ggplot2) package.\n3. provides an R interface to your instrument raw data.\n4. ships with an example [shiny application](http://fgcz-ms-shiny.uzh.ch:8080/bfabric_rawDiag/).\n\n## 1 Requirements \n\n### 1.1 Thermo License agreement\n\naccept the [Thermo Fisher RawFileReader License agreement](https://github.com/fgcz/rawDiag/blob/master/inst/docker/ThermoRawFileReader/RawFileReaderLicense.doc).\n\n### 1.2 System Requirements \n\na Windows/Linux/MacOSX x64 platform \n\n.NET Framework and R\n\n- https://www.mono-project.com/ (>4.0.22) for (Linux and MacOSX),\n- .NET Framework 4.5.1 or higher (Windows),\n- R (>3.4.0); please do not use R (3.5.0) on Windows! There is an `system2` issue,\n- install https://CRAN.R-project.org/package=devtools\n- if you want support for [Open File Standards](http://www.psidev.info/) install the [mzR](http://bioconductor.org/packages/mzR/) package. \n\n\n## 2 Installation guide\n\nTo ensure the proper function of this R package please check \nif all the [requirements](README.md#1-system-requirements) are \nfullfilled prior to using it. \n\n### 2.1 Install \nrun R\n```{r}\n#R\n \n# R package requirements\npkgs <- c( 'devtools',\n 'dplyr',\n 'ggplot2',\n 'hexbin',\n 'magrittr',\n 'parallel',\n 'protViz',\n 'rmarkdown',\n 'RSQLite',\n 'scales',\n 'shiny',\n 'tidyr',\n 'tidyverse')\npkgs <- pkgs[(!pkgs %in% unique(installed.packages()[,'Package']))]\nif(length(pkgs) > 0){install.packages(pkgs)}\n\n# Installation of rawDiag\ninstall.packages('http://fgcz-ms.uzh.ch/~cpanse/rawDiag_0.0.10.tar.gz')\n\n# Testing - \"Hello, world!\"\nlibrary(rawDiag)\n(rawfile <- file.path(path.package(package = 'rawDiag'), 'extdata', 'sample.raw'))\nsystem.time(RAW <- read.raw(file = rawfile))\ndim(RAW)\nsummary.rawDiag(RAW)\nPlotScanFrequency(RAW)\n\n# read all dimensions\ndim(RAW)\nRAW <- read.raw(file = rawfile, rawDiag = FALSE)\ndim(RAW)\n```\n\n### 2.2. If you have problems\n\n**If your installation does not work with the below-mentioned instructions, do not hesitate to contact us via [Email, SUBJECT `help request rawDiag package`](mailto:cp@fgcz.ethz.ch?SUBJECT=request%20current%20rawDiag%20package).**\n\nPlease include the output of the `sessInfo()` command line call.\n```{r}\nsessionInfo()\n```\n\n### 2.3 Install from GitHub (only for developers)\n\nthe following code downloads and installs the R package from the Github without the required third party .dll files:\nplease note: due to the data size (>=40MB) download can take a while\n\n```{r}\n# install.packages(\"devtools\")\nlibrary(\"devtools\")\ndevtools::install_github(\"fgcz/rawDiag\", build_vignettes = FALSE)\n```\n\nThe [New RawFileReader from Thermo Fisher Scientific](http://planetorbitrap.com/rawfilereader)\nhas to be downloaded and installed separately in order to be able to directly read Thermo raw-files (by using the R function `read.raw`).\n\nTo install [the New RawFileReader .Net assembly](http://planetorbitrap.com/rawfilereader) follow the installation instructions provided by Thermo Fisher Scientific.\n\n### 2.4 Typical install time on a \"normal\" desktop computer\n\n* Thermo RawFileReader dll: 1sec to 30 minutes\n* the rawDiag package through github: 10 minutes \n\n### 2.5 Platforms and versions the software has been tested on\n\nThe package [JPR.R1](https://github.com/fgcz/rawDiag/tree/JPR.R1) release has been tested on the following platforms using [RStudio](https://www.rstudio.com/):\n\n|platform|platform version|R version|note|\n| :------- |:--------------|:------|:------- |\n|Linux| Debian 8 (jessie) | 3.4.3 | [Demo system](http://fgcz-ms-shiny.uzh.ch:8080/bfabric_rawDiag/)|\n|Linux | Debian 10 ([buster](https://www.debian.org/releases/testing/releasenotes)) | 3.5.0 | CP |\n|Linux| bioconductor/devel_proteomics2| 2017-12-31 r73996 | [dockerhub](https://hub.docker.com/r/cpanse/rawdiag/builds/) |\n|Windows | 7 x64| 3.4.1 |CT|\n|Windows | 10 x64| 3.4.4 |CP virtual box|\n|Windows | Server 2012 R2 x64 | 3.4.4|CP|\n|Windows | 10 x64 | 3.4.3 | WEW |\n|Windows | 10 x64 | R Open 3.5.0 | WEW |\n|MacOSX | 10.13.5 (17F77)|3.4.2|CP|\n|MacOSX | 10.11.6 (15G20015)|3.4.3 |JG|\n|MacOSX | 10.13.4 (17E202)|3.4.4|CP|\n\n\n## 3 Demonstration\n\n### 3.1 R commandline code snippet\n\n\"Hello; World!\" example on the R command line\n\n```{r}\nlibrary(rawDiag)\ndata(WU163763)\nPlotScanFrequency(WU163763, method='overlay')\nPlotPrecursorHeatmap(WU163763)\nPlotMassDistribution(WU163763\n```\n\n### 3.2 An interactive shiny example\n\n#### in your local R shell\n```{r}\n# install.packages(\"shiny\")\n# install.packages(\"DT\")\nlibrary(shiny)\nrawDiag_shiny <- system.file('shiny', 'demo', package = 'rawDiag')\nshiny::runApp(rawDiag_shiny, display.mode = 'normal')\n```\n\n#### using the docker image\n\nsource: [dockerhub](https://hub.docker.com/r/cpanse/rawdiag/)\n\n```\ndocker pull cpanse/rawdiag \\\n&& docker run -it -p 8787:8787 cpanse/rawdiag R -e \"library(shiny); \\\n rawDiag_shiny <- system.file('shiny', 'demo', package = 'rawDiag'); \\\n shiny::runApp(rawDiag_shiny, display.mode = 'normal', port=8787, host='0.0.0.0')\"\n```\n\nconnect with your web browser to `http://yourdockerhostname:8787`\n\n### 3.3 using the `read.raw` method\n\ntaken from the `?read.raw` man page.\n```{r}\n(rawfile <- file.path(path.package(package = 'rawDiag'), 'extdata', 'sample.raw'))\nsystem.time(RAW <- read.raw(file = rawfile))\n \nsummary.rawDiag(RAW)\nPlotScanFrequency(RAW)\n \ndim(RAW)\n# now read all dimensions\nRAW <- read.raw(file = rawfile, rawDiag = FALSE)\ndim(RAW)\n```\n\n## 4 Instructions for use\n\nread the vignettes.\n\n```{r}\nbrowseVignettes('rawDiag')\n```\n\nthe documentation of the function is available through the R man pages.\n\n## 5 Useful links\n- http://planetorbitrap.com/rawfilereader\n- [screen recording (3:02 minutes, size 47MB, no audio track)](http://fgcz-ms.uzh.ch/~cpanse/PAPERS/pr-2018-001736.mov)\n- [shiny demo on our compute server](http://fgcz-ms-shiny.uzh.ch:8080/rawDiag-demo/)\n- *rawDiag - an R package supporting rational LC-MS method optimization for bottom-up proteomics*\nChristian Trachsel, Christian Panse, Tobias Kockmann, Witold Eryk Wolski, Jonas Grossmann, Ralph Schlapbach\nbioRxiv 304485; doi: https://doi.org/10.1101/304485\n(manuscript submitted to Journal of Proteome Research; **pr-2018-001736**).\n\n- [MassIVE MSV000082389](https://massive.ucsd.edu/ProteoSAFe/dataset.jsp?task=b231e78d674345798ebe50e46a9a3a93)\n\n- [ASMS 2018 poster as PDF(1.8M, md5=dab9388c1a465d931e9d2345119a2827)](http://fgcz-ms.uzh.ch/~cpanse/ASMS2018_ID291250.pdf)\n","has_starred","hub_user","immutable_tags_settings",{"_75":11,"_76":77},"enabled","rules",[78],".*","is_automated","permissions",{"_82":21,"_83":11,"_84":11},"read","write","admin","user","storage_size",6975448116,"orgData","recentTags",[91],{"_92":44,"_93":94,"_95":96,"_97":98,"_99":100,"_50":118,"_119":94,"_120":33,"_121":56,"_57":122,"_123":124,"_125":109,"_126":118,"_127":65,"_128":21},"content_type","creator",373508,"full_size",4396431163,"id",29030982,"images",[101],{"_102":103,"_104":105,"_106":107,"_108":109,"_110":111,"_112":113,"_114":107,"_115":-5,"_116":96,"_63":65,"_117":-5},"architecture","amd64","digest","sha256:4aaeaa825cc926a9fbcfbb18fe6e30100a62c029ad7b35e2151469297287bd33","features","","last_pulled","2026-09-26T19:08:15.186254518Z","last_pushed","2018-08-21T12:42:59Z","os","linux","os_features","os_version","size","variant","2018-08-21T12:42:58.49207Z","last_updater","last_updater_username","media_type","latest","repository",5609378,"tag_last_pulled","tag_last_pushed","tag_status","v2","sbxKitMetadata","isPotentialSpam","isHubSbxKitsEnabled","showSbxLogoOverride","sbxTrademarkText","displaySecurityMetadata","tagAttestations","tagsHaveAttestations",[],"selectedTag","attestationsUrl","routes/_layout.r.$namespace.$reponame.tags",{"_38":142,"_149":150,"_136":159,"_160":11},{"_40":143,"_42":144,"_45":46,"_47":48,"_49":11,"_50":51,"_52":53,"_54":145,"_57":35,"_32":33,"_58":59,"_60":44,"_61":62,"_63":62,"_64":65,"_66":-5,"_67":68,"_69":70,"_71":11,"_72":33,"_73":146,"_79":21,"_80":148,"_85":33,"_86":87},[],[44],[56],{"_75":11,"_76":147},[78],{"_82":21,"_83":11,"_84":11},"tags",{"_151":62,"_152":-5,"_153":-5,"_154":155},"count","next","previous","results",[156],{"_92":44,"_93":94,"_95":96,"_97":98,"_99":157,"_50":118,"_119":94,"_120":33,"_121":56,"_57":122,"_123":124,"_125":109,"_126":118,"_127":65,"_128":21},[158],{"_102":103,"_104":105,"_106":107,"_108":109,"_110":111,"_112":113,"_114":107,"_115":-5,"_116":96,"_63":65,"_117":-5},[],"canDeleteTags","actionData","errors"]

cpanse/rawdiag

Tags for cpanse/rawdiag