scoper

Spectral Clustering-Based Method for Identifying B Cell Clones

Provides a computational framework for B cell clones identification from adaptive immune receptor repertoire sequencing (AIRR-Seq) datasets. Three models are included (identical, hierarchical, and spectral) that perform clustering among sequences of BCRs/IGs (B cell receptors/immunoglobulins) which share the same V gene, J gene and junction length. Nouri N and Kleinstein SH (2018) <doi: 10.1093/bioinformatics/bty235>. Gupta NT, et al. (2017) <doi: 10.4049/jimmunol.1601850>.

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Description file content

Package
scoper
Type
Package
Version
0.2.0
Date
2019-08-05
Title
Spectral Clustering-Based Method for Identifying B Cell Clones
Description
Provides a computational framework for B cell clones identification from adaptive immune receptor repertoire sequencing (AIRR-Seq) datasets. Three models are included (identical, hierarchical, and spectral) that perform clustering among sequences of BCRs/IGs (B cell receptors/immunoglobulins) which share the same V gene, J gene and junction length. Nouri N and Kleinstein SH (2018) . Gupta NT, et al. (2017) .
License
CC BY-SA 4.0
URL
BugReports
https://bitbucket.org/kleinstein/scoper/issues
LazyData
true
BuildVignettes
true
VignetteBuilder
knitr
Encoding
UTF-8
SystemRequirements
C++11
Depends
R (>= 3.1.2), ggplot2 (>= 3.2.0)
Imports
alakazam (>= 0.3.0), shazam (>= 0.2.0), doParallel, foreach, dplyr (>= 0.8.1), Rcpp (>= 0.12.12), seqinr, data.table, stringi, stringr, methods, stats, rlang
LinkingTo
Rcpp
Suggests
knitr, rmarkdown, testthat
RoxygenNote
6.1.1
Collate
'Data.R' 'Scoper.R' 'Functions.R' 'RcppExports.R'
NeedsCompilation
yes
Packaged
2019-08-05 17:52:55 UTC; nima
Author
Nima Nouri [aut, cre], Jason Vander Heiden [ctb], Steven Kleinstein [aut, cph]
Maintainer
Nima Nouri
Repository
CRAN
Date/Publication
2019-08-05 21:50:02 UTC

install.packages('scoper')

0.2.0

4 months ago

https://scoper.readthedocs.io

Nima Nouri

CC BY-SA 4.0

Depends on

R (>= 3.1.2), ggplot2 (>= 3.2.0)

Imports

alakazam (>= 0.3.0), shazam (>= 0.2.0), doParallel, foreach, dplyr (>= 0.8.1), Rcpp (>= 0.12.12), seqinr, data.table, stringi, stringr, methods, stats, rlang

Suggests

knitr, rmarkdown, testthat

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