hahmmr

1.0.0

Haplotype-Aware Hidden Markov Model for RNA

1packages depend

4.9Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Teng GaoFirst published 2023-10-251 releasesCRAN page ↗

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/.

Install

R (CRAN)Ubuntu (r2u)

install.packages("hahmmr", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-hahmmr

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

Health

CRAN checks

13OK

Slowest check: 4.2 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.02

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 217 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

4.9K

CRAN downloads in the past year

Rank #9,560 · ~13/day · ~406/mo

Releases R versions

Daily download trend is not available in this view yet.

39730 days

1.2K90 days

4.9K1 year

Compare downloads with other packages →

Also on438 r2u725 bioconda

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (12)

data.table dplyr GenomicRanges ggplot2 glue IRangesmethodspatchwork Rcpp stringr tibble zoo

LinkingTo (3)

Rcpp RcppArmadillo roptim

Suggests (2)

ggrastr testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

numbat

Code & Tests

Datasets

People & History

People (3)

Maintainer (1)

Teng Gao

Author, Maintainer

Authors (3)

Teng Gao

Author, Maintainer

Evan Biederstedt

Author

Peter Kharchenko

Author

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
1.0.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2023-10-25
Total releases: 1 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1.0
Bundled data: 2.6 MB / 17 files
Download size: 2.6 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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