hahmmr: Haplotype-Aware Hidden Markov Model for RNA

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/>.

Version: 1.0.0
Depends: R (≥ 4.1.0)
Imports: data.table, dplyr, GenomicRanges, ggplot2, glue, IRanges, methods, patchwork, Rcpp, stringr, tibble, zoo
LinkingTo: Rcpp, RcppArmadillo, roptim
Suggests: ggrastr, testthat
Published: 2023-10-25
Author: Teng Gao ORCID iD [aut, cre], Evan Biederstedt [aut], Peter Kharchenko [aut]
Maintainer: Teng Gao <tgaoteng at gmail.com>
License: MIT + file LICENSE
NeedsCompilation: yes
Materials: README
CRAN checks: hahmmr results

Documentation:

Reference manual: hahmmr.pdf

Downloads:

Package source: hahmmr_1.0.0.tar.gz
Windows binaries: r-prerel: hahmmr_1.0.0.zip, r-release: hahmmr_1.0.0.zip, r-oldrel: hahmmr_1.0.0.zip
macOS binaries: r-prerel (arm64): hahmmr_1.0.0.tgz, r-release (arm64): hahmmr_1.0.0.tgz, r-oldrel (arm64): hahmmr_1.0.0.tgz, r-prerel (x86_64): hahmmr_1.0.0.tgz, r-release (x86_64): hahmmr_1.0.0.tgz

Reverse dependencies:

Reverse imports: numbat

Linking:

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