R Observatory: Metrics for VAM version 1.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

VAM

1.1.0

Variance-Adjusted Mahalanobis

2packages depend

10.3Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by H. Robert FrostFirst published 2021-01-147 releasesCRAN page ↗

Contains logic for cell-specific gene set scoring of single cell RNA sequencing data.

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("VAM", 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-vam

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

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-VAM

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-VAM

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

2NOTE11OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 3.1 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

3

Dependencies · direct

Check history

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 20%

Downloads

10.3K

CRAN downloads in the past year

Rank #4,556 · ~28/day · ~857/mo

Releases R versions

Daily download trend is not available in this view yet.

47130 days

1.7K90 days

10.3K1 year

Compare downloads with other packages →

Also on154 r2u21 autocran1.3K conda_forge27 c2d4u

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Depends (3)

R >= 3.6.0MASSMatrix

Imports (1)

methods

LinkingTo (0)

none

Suggests (3)

Seurat SeuratObject sctransform (>= 0.3.2)

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

0indirect

STREAK scaper

Code & Tests

People & History

People (0)

Author records are not tracked yet for this package.

Listed in earlier versions (1)

H. Robert Frost

no longer listed · 0.4.0 to 1.1.0

Package Timeline

7 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.1.0Latest
2023-11-05 · current release · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
1.0.0
2021-09-07 · diff ↗
0.5.3
2021-07-20 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.5.2
2021-03-15 · diff ↗
0.5.1
2021-02-09 · diff ↗
0.5.0
2021-02-01 · diff ↗
0.4.0
2021-01-14
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-01-14
Total releases: 7 / 5 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.6.0
Download size: 1.7 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("VAM")

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for VAM version 1.1.0 [Data set]. HJJB, LLC. Data release v2026-08-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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