R Observatory: Metrics for shaman version 2.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

shaman

2.1.1Package record

Sampling Hi-C Contact Matrices for Aparametric Normalization

0packages depend

208downloads / year

63.1%test coverage

10/10flavors OK

Overview

About

Maintained by Aviezer LifshitzCRAN page ↗GitHub ↗Website ↗Issues ↗

Generate expected Hi-C (genome-wide chromosome conformation capture) data maintaining marginal coverage, and the decay in contact probability with increasing genomic distance. Expected Hi-C data is used for normalization and graphical presentation of statistical significance of observed Hi-C contact enrichments. The method is described in Mendelson Cohen et al. (2017) doi:10.1101/187203.

Changes in 2.1.1

Fixed a compiler warning from GCC 16 (-Wstringop-overflow).

From NEWS.md in the release

Install

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

install.packages("shaman", 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("tanaylab/shaman")

Development version from tanaylab/shaman. Installs pak first if it is not already available.

# 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-shaman

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-shaman

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

10OK

CRAN check page ↗

Slowest check: 5.3 min · r-release-macos-x86_64

Status changes

OK10 OK2026-10-25
WARNING5 OK, 1 WARNING2026-10-17

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.1.1

READMEYes · 417 wordsVignettesYes · 2 · staticNEWSYes · 100% structured · mentions 2.1.1Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 24 (3 internal)includes a package overview page
Examples that run: 100%16 run in a plain check
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (2)

How these are measured

Downloads

208

CRAN downloads in the past year

Rank #25,517 · ~1/day · ~17/mo

Releases R versions

Daily download trend is not available in this view yet.

20830 days

20890 days

2081 year

Compare downloads with other packages →

Also on382 bioconda

How downloads are counted

Repository

tanaylab/shaman ↗Organization: tanaylab

6Stars

1Forks

5Open issues

0Open PRs

2Releases

223Commits

2Commit identities

mishahi-c

223 commits · Last activity 2026-10-18 · Default branch at 2.1.1.9000, ahead of CRAN 2.1.1 (checked 2026-10-25)

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 5

Releases over time

2026-10-16 · 12026-10-18 · 2

How these are measured

PracticesBeta

9 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/tanaylab/shaman on 2026-10-25.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux and macOS, and on R-devel

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-18 · The repository has a site deploy workflow

pkgdown site last built 2026-10-18

CRAN release process (1)

cran-comments.md

Lint, format, editor (1)

RStudio project

Show all practicesHide 1 practice

Git structural (1)

.gitattributes

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

Dependencies

Declared dependencies

13 external dependencies (excludes base and recommended)

Installing shaman adds 30 packages (19 with compiled code, 36 MB of source tarballs). Heaviest: stringi 11 MB, ggplot2 6.0 MB, data.table 5.7 MB.

Depends (1)

R >= 4.0.0

Imports (9)

misha Rcpp RANN data.table ggplot2 reshape2gridplyrparallel

LinkingTo (1)

Rcpp

Suggests (5)

knitr testthat rmarkdown Gviz foreach

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (4)

Aviezer Lifshitz

Author, Maintainer since 2.1.0 (2026)

Netta Mendelson Cohen

Author

Amos Tanay

Author

Weizmann Institute of Science

Copyright holder

Releases (2)

Pick two releases to compare their code metrics.

2.1.1Latest
record
2026-10-18 · current release · diff ↗ ·
listed once in CRAN's queue
Seen in one reading of CRAN's incoming queue, at 2026-10-18 07:37 UTC, so it stayed less than the time between readings.
2.1.0
record
2026-10-16 ·
10 days in CRAN's queue
Listed in CRAN's incoming queue from 2026-10-06 15:36 to 2026-10-16 07:45 UTC, in 45 readings.
R
R 4.6.0 released · 2026-04-24

Across CRAN, the median accepted release of the past year spent 22 hours in the queue, 90% under 11 days.How queue time is measured

Package metadata

First published: 2026-10-16
Total releases: 2 / 1 yrs
License: GPL
Minimum R: ≥ 4.0.0
Bundled data: 173 KB / 2 files
Download size: 1.6 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("shaman")

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

It points to 10.1101/187203.

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 shaman version 2.1.1 [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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