Showing 11 of total 11 results (show query)
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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.
Maintained by Katharina Waury. Last updated 1 months ago.
featureextractionproteomicssoftwarevisualization
25.2 match 4.65 score 10 scriptspharmaverse
pharmaversesdtm:SDTM Test Data for the 'Pharmaverse' Family of Packages
A set of Study Data Tabulation Model (SDTM) datasets from the Clinical Data Interchange Standards Consortium (CDISC) pilot project used for testing and developing Analysis Data Model (ADaM) datasets inside the pharmaverse family of packages. SDTM dataset specifications are described in the CDISC SDTM implementation guide, accessible by creating a free account on <https://www.cdisc.org/>.
Maintained by Edoardo Mancini. Last updated 3 days ago.
7.3 match 15 stars 7.40 score 143 scriptsvavrycuk-zz
PoDBAY:Vaccine Efficacy Estimation Package
Set of functions that implement the PoDBAY method, described in the publication 'A method to estimate probability of disease and vaccine efficacy from clinical trial immunogenicity data' by Julie Dudasova, Regina Laube, Chandni Valiathan, Matthew C. Wiener, Ferdous Gheyas, Pavel Fiser, Justina Ivanauskaite, Frank Liu and Jeffrey R. Sachs (NPJ Vaccines, 2021), <doi:10.1038/s41541-021-00377-6>.
Maintained by Julie Dudasova (MSD). Last updated 3 years ago.
8.6 match 3.30 score 10 scriptscran
PepMapViz:A Versatile Toolkit for Peptide Mapping, Visualization, and Comparative Exploration
A versatile R visualization package that empowers researchers with comprehensive visualization tools for seamlessly mapping peptides to protein sequences, identifying distinct domains and regions of interest, accentuating mutations, and highlighting post-translational modifications, all while enabling comparisons across diverse experimental conditions. Potential applications of 'PepMapViz' include the visualization of cross-software mass spectrometry results at the peptide level for specific protein and domain details in a linearized format and post-translational modification coverage across different experimental conditions; unraveling insights into disease mechanisms. It also enables visualization of major histocompatibility complex-presented peptides in different antibody regions predicting immunogenicity in antibody drug development.
Maintained by Zhenru Zhou. Last updated 4 months ago.
immunogenicitymassspectrometryproteomicspeptidomicssoftwarevisualization
10.5 match 2.70 scorepharmaverse
admiralvaccine:Vaccine Extension Package for ADaM in 'R' Asset Library
Programming vaccine specific Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in 'R'. Flat model is followed as per Center for Biologics Evaluation and Research (CBER) guidelines for creating vaccine specific domains. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team (2021), <https://www.cdisc.org/standards/foundational/adam/adamig-v1-3-release-package>). The package is an extension package of the 'admiral' package.
Maintained by Sukalpo Saha. Last updated 2 months ago.
3.4 match 6 stars 7.44 score 23 scriptsbioc
signifinder:Collection and implementation of public transcriptional cancer signatures
signifinder is an R package for computing and exploring a compendium of tumor signatures. It allows to compute a variety of signatures, based on gene expression values, and return single-sample scores. Currently, signifinder contains more than 60 distinct signatures collected from the literature, relating to multiple tumors and multiple cancer processes.
Maintained by Stefania Pirrotta. Last updated 2 months ago.
geneexpressiongenetargetimmunooncologybiomedicalinformaticsrnaseqmicroarrayreportwritingvisualizationsinglecellspatialgenesignaling
2.3 match 7 stars 6.40 score 15 scriptssistm
vici:Vaccine Induced Cellular Immunogenicity with Bivariate Modeling
A shiny app for accurate estimation of vaccine induced immunogenicity with bivariate linear modeling. Method is detailed in: Lhomme, Hejblum, Lacabaratz, Wiedemann, Lelievre, Levy, Thiebaut & Richert (2019). Submitted.
Maintained by Boris Hejblum. Last updated 9 months ago.
3.4 match 3.30 score 3 scriptslogin-
immunaut:Machine Learning Immunogenicity and Vaccine Response Analysis
Used for analyzing immune responses and predicting vaccine efficacy using machine learning and advanced data processing techniques. 'Immunaut' integrates both unsupervised and supervised learning methods, managing outliers and capturing immune response variability. It performs multiple rounds of predictive model testing to identify robust immunogenicity signatures that can predict vaccine responsiveness. The platform is designed to handle high-dimensional immune data, enabling researchers to uncover immune predictors and refine personalized vaccination strategies across diverse populations.
Maintained by Ivan Tomic. Last updated 5 months ago.
3.4 match 1.70 scorevavrycuk-zz
vaxpmx:Vaccines Pharmacometrics
Estimate vaccine efficacy (VE) using immunogenicity data. The inclusion of immunogenicity data in regression models can increase precision in VE. The methods are described in the publications "Elucidating vaccine efficacy using a correlate of protection, demographics, and logistic regression" and "Improving precision of vaccine efficacy evaluation using immune correlate data in time-to-event models" by Julie Dudasova, Zdenek Valenta, and Jeffrey R. Sachs (2024).
Maintained by Julie Dudasova (MSD). Last updated 4 months ago.
0.8 match 2.00 score