Introduction | Installation | User guide | Retrieving the protein features | Adding immunogens to the protein dataframe | Renaming an immunogen | Removing an immunogen | Visualizing the protein with the immunogens highlighted | Visualizing a specific immunogen | Evaluating the immunogens | Important Notes | References | Session info
Package: immunogenViewer 1.7.0
Katharina Waury
immunogenViewer: Visualization and evaluation of protein immunogens
Plots protein properties and visualizes position of peptide immunogens within protein sequence. Allows evaluation of immunogens based on structural and functional annotations to infer suitability for antibody-based methods aiming to detect native proteins.
Authors:
immunogenViewer_1.7.0.tar.gz
immunogenViewer_1.7.0.zip(r-4.7)immunogenViewer_1.7.0.zip(r-4.6)immunogenViewer_1.7.0.zip(r-4.5)
immunogenViewer_1.7.0.tgz(r-4.6-any)immunogenViewer_1.7.0.tgz(r-4.5-any)
immunogenViewer_1.7.0.tar.gz(r-4.7-any)immunogenViewer_1.7.0.tar.gz(r-4.6-any)
immunogenViewer_1.7.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
immunogenViewer/json (API)
| # Install 'immunogenViewer' in R: |
| install.packages('immunogenViewer', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/kathiwaury/immunogenviewer/issues
On BioConductor:immunogenViewer-1.7.0(bioc 3.24)immunogenViewer-1.6.0(bioc 3.23)
featureextractionproteomicssoftwarevisualization
Last updated from:39b2b138b2. Checks:8 NOTE, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 175 | ||
| linux-devel-x86_64 | NOTE | 265 | ||
| source / vignettes | OK | 232 | ||
| linux-release-x86_64 | NOTE | 282 | ||
| macos-release-arm64 | NOTE | 151 | ||
| macos-oldrel-arm64 | NOTE | 147 | ||
| windows-devel | NOTE | 188 | ||
| windows-release | NOTE | 187 | ||
| windows-oldrel | NOTE | 191 | ||
| wasm-release | OK | 167 |
Exports:addImmunogenaddImmunogenListevaluateImmunogengetProteinFeaturesplotImmunogenplotProteinremoveImmunogenrenameImmunogen
Dependencies:AnnotationDbiaskpassBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiostringsbitbit64blobcachemclicpp11crayoncurlDBIdbplyrdplyrfarverfastmapfilelockgenericsggplot2gluegtablehmshttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglifecyclemagrittrmemoisemimeopensslpatchworkpillarpkgconfigpngprettyunitsprogresspurrrR6rappdirsRColorBrewerrjsonconsrlangRSQLiteS4VectorsS7scalesSeqinfostringistringrsystibbletidyrtidyselectUniProt.wsutf8vctrsviridisLitewithrXVector
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Add an immunogen to the Protein DataFrame | addImmunogen |
| Add multiple immunogens to the Protein DataFrame | addImmunogenList |
| Create a summary DataFrame of the structural and functional properties of an immunogen | evaluateImmunogen |
| Retrieve structural and functional features to create a protein DataFrame | getProteinFeatures |
| Plot protein features of one immunogen region | plotImmunogen |
| Plot protein features with immunogens highlighted | plotProtein |
| Remove an existing immunogen | removeImmunogen |
| Rename an existing immunogen | renameImmunogen |
