ClustIRR
This is the development version of ClustIRR; for the stable release version, see ClustIRR.
Clustering of Immune Receptor Repertoires
Bioconductor version: Development (3.24)
ClustIRR analyzes repertoires of B- and T-cell receptors. It starts by identifying communities of immune receptors with similar specificities, based on the sequences of their complementarity-determining regions (CDRs). Next, it employs a Bayesian probabilistic models to quantify differential community occupancy (DCO) between repertoires, allowing the identification of expanding or contracting communities in response to e.g. infection or cancer treatment.
Author: Simo Kitanovski [aut, cre]
, Kai Wollek [aut]
Maintainer: Simo Kitanovski <simokitanovski at gmail.com>
citation("ClustIRR")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("ClustIRR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("ClustIRR")| Decoding T- and B-cell receptor repertoires with ClustIRR | HTML | R Script |
| Finding biological condition-specific changes in T- and B-cell receptor repertoires with ClustIRR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Bayesian, BiomedicalInformatics, Classification, Clustering, ImmunoOncology, MathematicalBiology, SingleCell, Software |
| Version | 1.11.0 |
| In Bioconductor since | BioC 3.18 (R-4.3) (3 years) |
| License | GPL-3 + file LICENSE |
| Depends | R (>= 4.3.0) |
| Imports | grDevices, igraph, methods, Rcpp (>= 0.12.0), RcppParallel (>= 5.0.1), reshape2, rstan (>= 2.18.1), rstantools (>= 2.4.0), stats, stringdist, utils, posterior, visNetwork, dplyr, tidyr, ggplot2, ggforce, scales, msa, Biostrings, RADanalysis, ggseqlogo, rBLAST |
| System Requirements | GNU make, ncbi-blast+ |
| URL | https://github.com/snaketron/ClustIRR |
| Bug Reports | https://github.com/snaketron/ClustIRR/issues |
See More
| Suggests | BiocStyle, knitr, testthat, ggrepel, patchwork, htmlwidgets |
| Linking To | BH (>= 1.66.0), Rcpp (>= 0.12.0), RcppEigen (>= 0.3.3.3.0), RcppParallel (>= 5.0.1), rstan (>= 2.18.1), StanHeaders (>= 2.18.0) |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ClustIRR_1.11.0.tar.gz |
| Windows Binary (x86_64) | ClustIRR_1.11.0.zip |
| macOS Binary (big-sur-x86_64) | ClustIRR_1.11.0.tgz |
| macOS Binary (sonoma-arm64) | ClustIRR_1.11.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ClustIRR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ClustIRR |
| Bioc Package Browser | https://code.bioconductor.org/browse/ClustIRR/ |
| Package Short Url | https://bioconductor.org/packages/ClustIRR/ |
| Package Downloads Report | Download Stats |