alakazam

Immunoglobulin Clonal Lineage and Diversity Analysis

Provides methods for high-throughput adaptive immune receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In particular, immunoglobulin (Ig) sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage. Citations: Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>, Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.

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Description file content

Package
alakazam
Type
Package
Version
0.3.0
Date
2019-07-17
Title
Immunoglobulin Clonal Lineage and Diversity Analysis
Description
Provides methods for high-throughput adaptive immune receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In particular, immunoglobulin (Ig) sequence lineage reconstruction, lineage topology analysis, diversity profiling, amino acid property analysis and gene usage. Citations: Gupta and Vander Heiden, et al (2017) , Stern, Yaari and Vander Heiden, et al (2014) .
License
CC BY-SA 4.0
URL
BugReports
https://bitbucket.org/kleinstein/alakazam/issues
LazyData
true
BuildVignettes
true
VignetteBuilder
knitr
Encoding
UTF-8
SystemRequirements
C++11
Depends
R (>= 3.1.2), ggplot2 (>= 2.0.0)
Imports
ape, dplyr (>= 0.8.1), graphics, grid, igraph (>= 1.0.0), lazyeval, Matrix, methods, progress, Rcpp (>= 0.12.12), readr, rlang, scales, seqinr, stats, stringi, tibble, tidyr, utils
LinkingTo
Rcpp
Suggests
knitr, rmarkdown, testthat
RoxygenNote
6.1.1
Collate
'Alakazam.R' 'AminoAcids.R' 'Classes.R' 'Core.R' 'Data.R' 'Diversity.R' 'Deprecated.R' 'Gene.R' 'Lineage.R' 'RcppExports.R' 'Sequence.R' 'Topology.R'
NeedsCompilation
yes
Packaged
2019-07-17 19:15:47 UTC; vandej27
Author
Jason Vander Heiden [aut, cre], Namita Gupta [aut], Susanna Marquez [ctb], Daniel Gadala-Maria [ctb], Ruoyi Jiang [ctb], Nima Nouri [ctb], Kenneth Hoehn [ctb], Julian Zhou [ctb], Steven Kleinstein [aut, cph]
Maintainer
Jason Vander Heiden
Repository
CRAN
Date/Publication
2019-07-18 11:20:13 UTC

install.packages('alakazam')

0.3.0

a month ago

http://alakazam.readthedocs.org

Jason Vander Heiden

CC BY-SA 4.0

Depends on

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

Imports

ape, dplyr (>= 0.8.1), graphics, grid, igraph (>= 1.0.0), lazyeval, Matrix, methods, progress, Rcpp (>= 0.12.12), readr, rlang, scales, seqinr, stats, stringi, tibble, tidyr, utils

Suggests

knitr, rmarkdown, testthat

Discussions