Imports: MASS, nlme, methods, isotone, stringr, prettyR, stats,
Description: Estimation and inference for linear models where some or all of the
fixed-effects coefficients are subject to order restrictions. This package uses
the robust residual bootstrap methodology for inference, and can handle some
structure in the residual variance matrix.
Authors@R: c(person("Casey M."  , "Jelsema", email="jelsema.casey@gmail.com", role=c("aut", "cre") ),
person("Shyamal D.", "Peddada", role="aut" ))
Maintainer: Casey M. Jelsema <jelsema.casey@gmail.com>

Depends: R (>= 4.0.0), shiny, lme4, MASS
Imports: nlme, methods, isotone, stringr, prettyR, stats, openxlsx,

Description: Estimation and inference for linear models where some or all of the fixed-effects coefficients are subject to order restrictions. This package uses the robust residual bootstrap methodology for inference, and can handle some structure in the residual variance matrix.
Author: Casey M. Jelsema, Shyamal D. Peddada

Authors@R: c(person("Davide", "Prandi", email = "davide.prandi@unitn.it",role = c("aut", "cre")),
person("Alessandro", "Romanel", email = "alessandro.romanel@unitn.it",role = c("ctb")),
person("Tarcisio", "Fedrizzi", email = "tarcisio.fedrizzi@unitn.it",role = c("ctb")))
Description: Analyze data from next-generation sequencing experiments on genomic samples. 'CLONETv2' offers a set of functions to compute allele specific copy number and clonality from segmented data and SNPs position pileup. The package has also calculated the clonality of single nucleotide variants given read counts at mutated positions. The package has been developed at the laboratory of Computational and Functional Oncology, Department of CIBIO, University of Trento (Italy), under the supervision of prof Francesca Demichelis. References: Prandi et al. (2014) <doi:10.1186/s13059-014-0439-6>; Carreira et al. (2014) <doi:10.1126/scitranslmed.3009448>.
Imports: parallel, sets, ggplot2, ggrepel, arules

Authors@R: c(person("Davide", "Prandi", email = "davide.prandi@unitn.it",role = c("aut")),
person("Tarcisio", "Fedrizzi", email = "tarcisio.fedrizzi@unitn.it",role = c("ctb")),
person("Yari", "Ciani", email = "yari.ciani@unitn.it",role = c("cre")))
Description: Analyze data from next-generation sequencing experiments on genomic samples. 'CLONETv2' offers a set of functions to compute allele specific copy number and clonality from segmented data and SNPs position pileup. The package has also calculated the clonality of single nucleotide variants given read counts at mutated positions. The package has been developed at the laboratory of Computational and Functional Oncology, Department of CIBIO, University of Trento (Italy), under the supervision of prof Francesca Demichelis. References: Prandi et al. (2014) <doi:10.1186/s13059-014-0439-6>; Carreira et al. (2014) <doi:10.1126/scitranslmed.3009448>; Romanel et al. (2015) <doi:10.1126/scitranslmed.aac9511>.
Imports: parallel, sets, ggplot2, ggrepel, arules, dbscan