R Observatory: Metrics for AmyloGram version 1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

AmyloGram needs biogram, which CRAN will archive unless its check problems are fixed by Nov 2.

AmyloGram

1.1Package record

Prediction of Amyloid Proteins

0packages depend

3.4Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Michal BurdukiewiczCRAN page ↗GitHub ↗Issues ↗

Predicts amyloid proteins using random forests trained on the n-gram encoded peptides. The implemented algorithm can be accessed from both the command line and shiny-based GUI.

Install

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

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("michbur/AmyloGram")

Development version from michbur/AmyloGram. Installs pak first if it is not already available.

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-amylogram

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

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-AmyloGram

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-AmyloGram

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Michal Burdukiewicz <michalburdukiewicz@gmail.com>’

Package CITATION file contains call(s) to old-style citEntry().  Please
use bibentry() instead.

Found the following URLs which should use \doi (with the DOI name only):
  File ‘AmyloGram-package.Rd’:
    https://doi.org/10.1038/s41598-017-13210-9

CRAN check page ↗

Slowest check: 1.9 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1

READMEYes · 71 wordsVignettesNoNEWSNoCitation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 9includes a package overview page
Examples that run: 100%2 run in a plain check
Exported functions with examples: 0%
Documented parameters: 100%
Return-value docs: 67%
Help pages citing references: 11%

How these are measured

Downloads

3.4K

CRAN downloads in the past year

Rank #8,845 · ~9/day · ~286/mo

Releases R versions

Daily download trend is not available in this view yet.

33530 days

1.1K90 days

3.4K1 year

Compare downloads with other packages →

Also on91 r2u23 autocran

How downloads are counted

Repository

michbur/amylogram ↗Account: michbur

9Stars

1Forks

2Open issues

0Open PRs

1Releases

53Commits

2Commit identities

53 commits · Last activity 2020-05-21 · Default branch at 1.2, ahead of CRAN 1.1 (checked 2026-10-21)

Responsiveness

not measured

Stars over time

2024-07-25 · 92026-07-07 · 9

How these are measured

PracticesBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/michbur/amylogram on 2026-10-21.

Continuous integration (1)

Travis CI (config file)

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

4 external dependencies (excludes base and recommended)

Installing AmyloGram adds 48 packages (30 with compiled code, 42 MB of source tarballs). Heaviest: bslib 5.6 MB, sp 4.3 MB, seqinr 3.4 MB.

Depends (1)

R >= 3.0.0

Imports (4)

biogram ranger seqinr shiny

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependencies facing archival

CRAN will archive these unless their check problems are fixed by the date shown. This package needs each one to install.

biogramfix by Nov 2

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (3)

Michal Burdukiewicz

Maintainer since 1.0 (2016), Author

Stefan Roediger

Contributor

Piotr Sobczyk

Contributor

Releases (2)

Pick two releases to compare their code metrics.

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
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
1.1Latest
record
2017-10-11 · current release · diff ↗
R
R 3.4.0 released · 2017-04-21
1.0
record
2016-09-24
R
R 3.3.0 released · 2016-05-03

Package metadata

First published: 2016-09-24
Total releases: 2 / 10 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.0.0
Bundled data: 257 KB / 3 files
Download size: 343 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("AmyloGram")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1038/s41598-017-13210-9.

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 AmyloGram version 1.1 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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