The hardware and bandwidth for this mirror is donated by METANET, the Webhosting and Full Service-Cloud Provider.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]metanet.ch.

shazam: Immunoglobulin Somatic Hypermutation Analysis

Provides a computational framework for analyzing mutations in immunoglobulin (Ig) sequences. Includes methods for Bayesian estimation of antigen-driven selection pressure, mutational load quantification, building of somatic hypermutation (SHM) models, and model-dependent distance calculations. Also includes empirically derived models of SHM for both mice and humans. Citations: Gupta and Vander Heiden, et al (2015) <doi:10.1093/bioinformatics/btv359>, Yaari, et al (2012) <doi:10.1093/nar/gks457>, Yaari, et al (2013) <doi:10.3389/fimmu.2013.00358>, Cui, et al (2016) <doi:10.4049/jimmunol.1502263>.

Version: 1.2.0
Depends: R (≥ 4.0), ggplot2 (≥ 3.4.0)
Imports: alakazam (≥ 1.3.0), ape, diptest, doParallel, dplyr (≥ 1.0), foreach, graphics, grid, igraph (≥ 1.5.0), iterators, KernSmooth, lazyeval, MASS, methods, parallel, progress, rlang, scales, seqinr, stats, stringi (≥ 1.1.3), tidyr, tidyselect, utils
Suggests: knitr, rmarkdown, testthat
Published: 2023-10-02
DOI: 10.32614/CRAN.package.shazam
Author: Mohamed Uduman [aut], Namita Gupta [aut], Susanna Marquez [aut, cre], Julian Zhou [aut], Nima Nouri [aut], Noah Yann Lee [aut], Ang Cui [ctb], Jason Vander Heiden [aut], Gur Yaari [aut], Steven Kleinstein [aut, cph]
Maintainer: Susanna Marquez <susanna.marquez at yale.edu>
BugReports: https://bitbucket.org/kleinstein/shazam/issues
License: AGPL-3
URL: http://shazam.readthedocs.io
NeedsCompilation: no
Citation: shazam citation info
Materials: README NEWS
CRAN checks: shazam results

Documentation:

Reference manual: shazam.pdf
Vignettes: Selection quantification
Distance to nearest neighbor
Mutation analysis
Simulating sequence mutations
SHM targeting models

Downloads:

Package source: shazam_1.2.0.tar.gz
Windows binaries: r-devel: shazam_1.2.0.zip, r-release: shazam_1.2.0.zip, r-oldrel: shazam_1.2.0.zip
macOS binaries: r-release (arm64): shazam_1.2.0.tgz, r-oldrel (arm64): shazam_1.2.0.tgz, r-release (x86_64): shazam_1.2.0.tgz, r-oldrel (x86_64): shazam_1.2.0.tgz
Old sources: shazam archive

Reverse dependencies:

Reverse imports: dowser, scoper

Linking:

Please use the canonical form https://CRAN.R-project.org/package=shazam to link to this page.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.