R Observatory: Metrics for palmid version 0.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

This package was removed from CRAN on 2023-09-16. Its history is shown below.

Reason: policy violation. On Internet access

Details below reflect version 0.0.3, its last release before removal.

palmid

0.0.3Package record

RdRP Analysis Suite

0packages depend

–downloads / year

–test coverage

–flavors OK

Overview

About

Maintained by Artem BabaianCRAN page ↗Website ↗

R Analysis suite for viral RNA dependent RNA polymerase (RdRP). Statistical and meta-data analysis of 'palmscan' output and 'palmDB'/ 'DIAMOND' alignment files. Cross reference an input RNA virus against 145,000 RdRP identified in the Serratus project.

Changes in 0.0.3

Initial release. palmid is a containerized analysis suite and R-package for the classification of **viral RNA-dependent RNA Polymerases (RdRP)** based on the **palmprint** sub-domain and the RNA viral palmprint database palmdb.

Features

Reading of palmscan and palmDB/DIAMOND-based alignment output files.
Automated access to the Serratus SQL-server and cross-database analysis of input sequences.
Taxonomic inference of input viral sequencing based on RdRP protein identity.
Geospatial and temporal analysis of virus-sequence matches.
Virus-associated host organism analysis of the Sequence Read Archive.
Containerized work environment for reproducible deployment.

From NEWS.md in the release

Install

R (source archive)

url <- "https://cran.r-project.org/src/contrib/Archive/palmid/palmid_0.0.3.tar.gz"
pkgFile <- "palmid_0.0.3.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (0.0.3) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

Health

CRAN checks

CRAN check results are not tracked yet.

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.0.3

READMEYes · 397 wordsVignettesNoNEWSYes · 67% structured · mentions 0.0.3Citation fileNoWebsiteYes

Help pages: 38
Examples that run: 76%22 run in a plain check · 5 only when donttest examples are enabled (R CMD check --as-cran) · 2 hold no code
Exported functions with examples: 85%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

How these are measured

Downloads

palmid Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on34 r2u

How downloads are counted

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Depends (3)

R >= 3.5.0dplyr ggplot2

Imports (20)

dbplyr downloadthis DBI DT ggplotify ggwordcloud ggExtragrDevicesgridExtra htmltools htmlwidgets leafletmethodsplotly rmarkdown RPostgreSQL scalesstatsutilsviridisLite

LinkingTo (0)

none

Suggests (3)

sf rnaturalearth rnaturalearthdata

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Artem Babaian

Author, Maintainer since 0.0.3 (2021)

Releases (1)

R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2023-09-16
policy violation On Internet access
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.0.3
record
2021-10-15
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2021-10-15
Total releases: 1 / 5 yrs
License: AGPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 350 KB / 4 files

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("palmid")

Format

Babaian, A. (n.d.). palmid: RdRP Analysis Suite (Version 0.0.3) [Computer software]. Retrieved October 26, 2026, from https://CRAN.R-project.org/package=palmid

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 palmid version 0.0.3 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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