Package: hahmmr
Title: Haplotype-Aware Hidden Markov Model for RNA
Version: 1.0.0
Authors@R: 
    c(person("Teng", "Gao", email = "tgaoteng@gmail.com", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-0196-689X")),
    person("Evan", "Biederstedt", email = "evan.biederstedt@gmail.com", role="aut"),
    person("Peter", "Kharchenko", email = "peter_kharchenko@hms.harvard.edu", role = "aut"))
Description: Haplotype-aware Hidden Markov Model for RNA (HaHMMR) is a method for detecting copy number variations (CNVs) from bulk RNA-seq data. Additional examples, documentations, and details on the method are available at <https://github.com/kharchenkolab/hahmmr/>.
Depends: R (>= 4.1.0)
biocViews:
Imports: data.table, dplyr, GenomicRanges, ggplot2, glue, IRanges,
        methods, patchwork, Rcpp, stringr, tibble, zoo
Suggests: ggrastr, testthat
LinkingTo: Rcpp, RcppArmadillo, roptim
NeedsCompilation: yes
License: MIT + file LICENSE
Encoding: UTF-8
RoxygenNote: 7.2.3
LazyData: true
Packaged: 2023-10-25 14:22:02 UTC; tenggao
Author: Teng Gao [aut, cre] (<https://orcid.org/0000-0002-0196-689X>),
  Evan Biederstedt [aut],
  Peter Kharchenko [aut]
Maintainer: Teng Gao <tgaoteng@gmail.com>
Repository: CRAN
Date/Publication: 2023-10-25 18:00:10 UTC
Built: R 4.4.3; x86_64-w64-mingw32; 2025-12-29 18:53:58 UTC; windows
Archs: x64
