Package: immunogenViewer 1.1.0

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:Katharina Waury [aut, cre]

immunogenViewer_1.1.0.tar.gz
immunogenViewer_1.1.0.zip(r-4.5)immunogenViewer_1.1.0.zip(r-4.4)immunogenViewer_1.1.0.zip(r-4.3)
immunogenViewer_1.1.0.tgz(r-4.4-any)immunogenViewer_1.1.0.tgz(r-4.3-any)
immunogenViewer_1.1.0.tar.gz(r-4.5-noble)immunogenViewer_1.1.0.tar.gz(r-4.4-noble)
immunogenViewer_1.1.0.tgz(r-4.4-emscripten)immunogenViewer_1.1.0.tgz(r-4.3-emscripten)
immunogenViewer.pdf |immunogenViewer.html✨
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-1.1.0(bioc 3.21)immunogenViewer-1.0.0(bioc 3.20)

featureextraction proteomics software visualization

4.65 score 9 scripts 66 downloads 7 exports 77 dependencies

Last updated 3 months agofrom:a57d054f08. Checks:1 OK, 4 NOTE, 2 ERROR. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Dec 27 2024
R-4.5-win	NOTE	Dec 31 2024
R-4.5-linux	NOTE	Dec 27 2024
R-4.4-win	NOTE	Dec 31 2024
R-4.4-mac	ERROR	Dec 31 2024
R-4.3-win	NOTE	Dec 31 2024
R-4.3-mac	ERROR	Dec 31 2024

Exports:addImmunogen evaluateImmunogen getProteinFeatures plotImmunogen plotProtein removeImmunogen renameImmunogen

Dependencies:AnnotationDbi askpass Biobase BiocBaseUtils BiocFileCache BiocGenerics Biostrings bit bit64 blob cachem cli colorspace cpp11 crayon curl DBI dbplyr digest dplyr fansi farver fastmap filelock generics GenomeInfoDb GenomeInfoDbData ggplot2 glue gtable hms httpcache httr IRanges isoband jsonlite KEGGREST labeling lattice lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme openssl patchwork pillar pkgconfig plogr png prettyunits progress purrr R6 RColorBrewer rjsoncons rlang RSQLite S4Vectors scales stringi stringr sys tibble tidyr tidyselect UCSC.utils UniProt.ws utf8 vctrs viridisLite withr XVector

Using immunogenViewer to evaluate and choose antibodies

Katharina Waury

Rendered fromimmunogenViewer_vignette.Rmdusingknitr::rmarkdownon Dec 27 2024.

Last update: 2024-05-31
Started: 2024-05-01

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Add an immunogen to the Protein DataFrame	addImmunogen
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