immunogenViewer
Science Score: 39.0%
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Low similarity (10.6%) to scientific vocabulary
Repository
Basic Info
- Host: GitHub
- Owner: kathiwaury
- License: apache-2.0
- Language: R
- Default Branch: main
- Size: 174 KB
Statistics
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
immunogenViewer
The package immunogenViewer is meant to support researchers in comparing and choosing suitable antibodies provided that information on the immunogen used to raise the antibody is available. When the immunogen of an antibody is known, its binding site within the protein antigen is defined and can be examined in detail. As antibodies raised against peptide immunogens often do not function properly when used to detect natively folded proteins (Brown et al. 2011), examination of the position of the immunogen within the full-length protein can provide insights. Using immunogenViewer provides an easy approach to visualize, evaluate and compare immunogens within the full-length sequence of a protein. Information on structural and functional annotations of the immunogen and thus antibody binding site can tell the user if an antibody is potentially useful for native protein detection (Trier et al. 2012, Waury et al. 2022).
Specifically, immunogenViewer can be used to retrieve protein features for a protein of interest using an API call to the UniProtKB and PredictProtein databases. The features are saved on a per-residue level in a dataframe. One or several immunogens can be associated with the protein. The immunogen(s) can then be visualized and evaluated regarding their structure and other annotations that can influence successful antibody recognition within the full-length protein. A summary report of the immunogen can be created to easily compare and select favorable immunogens and their respective antibodies. This package should be used as a pre-selection step to exclude unsuitable antibodies early on. It does not replace comprehensive antibody validation. For more information on validation, please refer to other excellent resources (Roncador et al. 2015, Voskuil et al. 2020).
Installation
The package can currently be installed directly from GitHub.
{r installation, eval=FALSE}
install.packages("devtools")
devtools::install_github("kathiwaury/immunogenViewer")
library(immunogenViewer)
Package usage
The package can be used to retrieve relevant properties for a protein of interest which are saved in a protein dataframe. Immunogens can be added to the protein dataframe via position or sequence information.
{r features, eval=FALSE}
protein <- getProteinFeatures("Q9NZC2")
protein <- addImmunogen(protein, start = 196, end = 230, name = "HPA010917")
protein <- addImmunogen(protein, seq = "HGQKPGTHPPSELD", name = "EB07921")
The full protein sequence with all properties and with the immunogens highlighted can be visualized.
{r protein, eval=FALSE}
plotProtein(protein)
Specific immunogens within the protein sequence can also be viewed.
{r immunogen, eval=FALSE}
plotImmunogen(protein, "ABIN2783734")
For detailed use instructions, please see the vignette and manual.
Contact and bug reports
If you encounter a bug or any issue, please open an issue here. For any other questions or comments, please contact Katharina Waury (k.waury@vu.nl).
Owner
- Name: Katharina Waury
- Login: kathiwaury
- Kind: user
- Location: The Netherlands
- Company: VU Amsterdam
- Repositories: 1
- Profile: https://github.com/kathiwaury
PhD Candidate in the Bioinformatics group, VU Amsterdam
GitHub Events
Total
- Push event: 2
Last Year
- Push event: 2
Committers
Last synced: 11 months ago
Top Committers
| Name | Commits | |
|---|---|---|
| Katharina Waury | 4****y@u****m | 27 |
| Giulia Crocioni | 5****2@u****m | 4 |
| Waury | k****0@l****r | 3 |
| Waury | k****0@n****r | 3 |
| Waury | k****0@l****r | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: about 1 year ago
All Time
- Total issues: 2
- Total pull requests: 1
- Average time to close issues: about 1 month
- Average time to close pull requests: 11 days
- Total issue authors: 1
- Total pull request authors: 1
- Average comments per issue: 0.5
- Average comments per pull request: 0.0
- Merged pull requests: 1
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- PabRod (2)
Pull Request Authors
- gcroci2 (1)
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Packages
- Total packages: 1
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Total downloads:
- bioconductor 1,693 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 2
- Total maintainers: 1
bioconductor.org: immunogenViewer
Visualization and evaluation of protein immunogens
- Homepage: https://github.com/kathiwaury/immunogenViewer
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/immunogenViewer/inst/doc/immunogenViewer.pdf
- License: Apache License (>= 2)
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Latest release: 1.1.1
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 2.10 depends
- ggplot2 * imports
- httr * imports
- jsonlite * imports
- patchwork * imports
- BiocStyle * suggests
- DT * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat >= 3.0.0 suggests