scoper

Spectral Clustering-Based Method for Identifying B Cell Clones

Provides a computational framework for unsupervised identification B cell clones from adaptive immune receptor repertoire sequencing (AIRR-Seq) datasets. This method is based on spectral clustering of the junction sequences of B cell receptors (BCRs, also referred to as Immunoglobulins, (Igs)) that share the same V gene, J gene and junction length.

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Description file content

Package
scoper
Type
Package
Version
0.1.0
Date
2018-10-04
Title
Spectral Clustering-Based Method for Identifying B Cell Clones
Description
Provides a computational framework for unsupervised identification B cell clones from adaptive immune receptor repertoire sequencing (AIRR-Seq) datasets. This method is based on spectral clustering of the junction sequences of B cell receptors (BCRs, also referred to as Immunoglobulins, (Igs)) that share the same V gene, J gene and junction length.
License
CC BY-SA 4.0
URL
BugReports
https://bitbucket.org/kleinstein/scoper/issues
LazyData
true
BuildVignettes
true
VignetteBuilder
knitr
Encoding
UTF-8
Depends
R (>= 3.1.2), ggplot2 (>= 2.0.0)
Imports
alakazam (>= 0.2.11), shazam (>= 0.1.10), doParallel, foreach, dplyr (>= 0.7.0), stringi, methods, stats, iterators, lazyeval
Suggests
knitr, rmarkdown, testthat
RoxygenNote
6.1.0
Collate
'Data.R' 'Scoper.R' 'Functions.R'
NeedsCompilation
no
Packaged
2018-10-04 20:58:03 UTC; nima
Author
Nima Nouri [aut, cre], Jason Vander Heiden [ctb], Steven Kleinstein [aut, cph]
Maintainer
Nima Nouri
Repository
CRAN
Date/Publication
2018-10-14 17:00:03 UTC

install.packages('scoper')

0.1.0

a month ago

https://scoper.readthedocs.io

Nima Nouri

CC BY-SA 4.0

Depends on

R (>= 3.1.2), ggplot2 (>= 2.0.0)

Imports

alakazam (>= 0.2.11), shazam (>= 0.1.10), doParallel, foreach, dplyr (>= 0.7.0), stringi, methods, stats, iterators, lazyeval

Suggests

knitr, rmarkdown, testthat

Discussions