R Observatory: Metrics for misha version 5.11.23

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

misha

5.11.23Package record

Toolkit for Analysis of Genomic Data

1packages depend

2.8Kdownloads / year

58.0%test coverage

6/10flavors OK

Overview

About

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

A toolkit for analysis of genomic data. The 'misha' package implements an efficient data structure for storing genomic data, and provides a set of functions for data extraction, manipulation and analysis. Some of the 2D genome algorithms were described in Yaffe and Tanay (2011) doi:10.1038/ng.947.

Changes in 5.11.23

Packaging fix for the CRAN submission; no user-visible changes.

From NEWS.md in the release

Install

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

install.packages("misha", 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/misha")

Development version from tanaylab/misha. 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-misha

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-misha

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-misha

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

4NOTE6OK

Check messages

NOTEdependencies in R coder-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Base package in Suggests/Enhances imported in NAMESPACE:
  ‘stats’

CRAN check page ↗

Slowest check: 13.0 min · r-release-linux-x86_64

Status changes

NOTE6 OK, 4 NOTENow
NOTE9 OK, 1 NOTE2026-09-12
OK10 OK2026-08-05
NOTE9 OK, 1 NOTE2026-08-01
OK10 OK2026-06-09
WARNING9 OK, 1 WARNING2026-06-08

Show 7 earlier changesHide 7 earlier changes

ERROR9 OK, 1 ERROR2026-06-07
OK10 OK2026-05-11
WARNING9 OK, 1 WARNING2026-05-10
OK10 OK2026-05-02
NOTE5 OK, 6 NOTE2026-04-10
ERROR4 OK, 6 NOTE, 1 ERROR2026-04-09
NOTE9 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 5.11.23

READMEYes · 461 wordsVignettesYes · 4 · dynamicNEWSYes · 100% structured · mentions 5.11.23Citation fileNoWebsiteYes · pkgdown

Help pages: 183 (7 internal)includes a package overview page
Examples that run: 81%121 run in a plain check · 3 only when donttest examples are enabled (R CMD check --as-cran) · 24 never run · 1 hold no code
Exported functions with examples: 85%
Documented parameters: 94%
Return-value docs: 99%
Help pages citing references: 0%

Vignettes (4)

Database Formats and Multi-Contig Support HTML
Genomes HTML
Manual HTML
Misha Basics (Short Guide) HTML

How these are measured

Downloads

2.8K

CRAN downloads in the past year

Rank #15,558 · ~8/day · ~235/mo

Releases R versions

Daily download trend is not available in this view yet.

26730 days

78990 days

2.8K1 year

Compare downloads with other packages →

Also on461 r2u7 autocran5.5K bioconda

How downloads are counted

Repository

tanaylab/misha ↗Organization: tanaylab

4Stars

2Forks

1Open issues

5Open PRs

61Releases

1,195Commits

3Commit identities

genomic-data-analysis

1,195 commits · Last activity 2026-10-21 · Default branch at 5.13.3, ahead of CRAN 5.11.23 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 90%
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2022-11-02 · 42026-07-07 · 4

How these are measured

PracticesBeta

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

Checks run against github.com/tanaylab/misha on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

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

Governance and community (1)

Contributing guide

Docs source (4)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-10-21 · The repository has a site deploy workflow

pkgdown site last built 2026-10-21

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Show all practicesHide 1 practice

Lint, format, editor (1)

Lint workflow

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

AI coding toolsBeta

This repository shows signs of AI coding tools.

Aiderfirst seen 2025-02-24
Named in .gitignore: .aider*
Claude Codefirst seen 2025-08-31
Named in .Rbuildignore: .claude, CLAUDE.md
Named in .gitignore: .claude
Pull request it wrote: opened by a project member
Codexfirst seen 2026-04-16
Named in .gitignore: .codex

Shared conventions any agent may read, so they name no particular tool.

Seen in the repository: AGENTS.md

How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

Installing misha adds 5 packages (5 with compiled code, 1.5 MB of source tarballs). Heaviest: curl 714 KB, magrittr 275 KB, digest 231 KB.

Depends (1)

R >= 3.0.0

Imports (8)

magrittr curl digest psparallelutilstoolsyaml

LinkingTo (0)

none

Suggests (12)

data.table dplyr glue knitr readr rmarkdown spellingstatsstringr testthat tibble withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

Imports 1

Depends, Imports or LinkingTo, most downloaded first

shaman

How these are counted

Code & Tests

People & History

People (5)

Aviezer Lifshitz

Author, Maintainer since 4.2.3 (2023)

Misha Hoichman

Author

Amos Tanay

Author

Eitan Yaffe

Author

Weizmann Institute of Science

Copyright holder

Releases (13)

Pick two releases to compare their code metrics.

5.11.23Latest
record
2026-08-24 · current release · diff ↗ ·
added 22 exports
gdb.build_genome, gdb.genome_info, gdb.install_gff3_converter, gdb.install_gtf_converter, gdb.install_intervals, gdb.list_genomes, gdb.unload, ggenome.implant, ggenome.transplant, gintervals.2d.intersect, gintervals.2d.union, gintervals.from_mat, gintervals.from_strings, gintervals.import_bed, gintervals.import_gff, gintervals.import_vcf, gintervals.to_mat, gseq.pwm_edits, gsynth.cell_merge, gsynth.forbid_kmer, gsynth.score, gvtrack.clear
R
R 4.6.0 released · 2026-04-24
5.6.6
record
2026-03-19 · diff ↗ ·
added 11 exports
gintervals.attr.export, gintervals.attr.get, gintervals.attr.import, gintervals.attr.set, gseq.read_homer, gseq.read_jaspar, gseq.read_meme, gsynth.convert, gtrack.2d.convert_to_indexed, gtrack.export_bedgraph, gtrack.export_bigwig
5.4.5
record
2026-02-20 · diff ↗ ·
added 1 export
gdb.export_fasta
5.4.0
record
2026-01-27 · diff ↗ ·
added 22 exports
gcor, gdataset.example_path, gdataset.info, gdataset.load, gdataset.ls, gdataset.save, gdataset.unload, gdb.create_linked, gintervals.dataset, gintervals.dbs, gseq.kmer.dist, gsynth.bin_map, gsynth.load, gsynth.random, gsynth.replace_kmer, gsynth.sample, gsynth.save, gsynth.train, gtrack.copy, gtrack.dataset, gtrack.dbs, gtrack.mv
5.3.2
record
2025-12-14 · diff ↗
5.3.1
record
2025-12-10 · diff ↗ ·
added 22 exports
gdb.convert_to_indexed, gdb.info, gdb.mark_cache_dirty, gintervals.2d.convert_to_indexed, gintervals.as_chain, gintervals.convert_to_indexed, gintervals.coverage_fraction, gintervals.covered_bp, gintervals.mark_overlaps, gintervals.neighbors.directional, gintervals.neighbors.downstream, gintervals.neighbors.upstream, gintervals.path, gintervals.random, gseq.comp, gseq.kmer, gseq.pwm, gseq.rev, gseq.revcomp, gtrack.convert_to_indexed, gtrack.path, gvtrack.filter
4.3.12
record
2025-08-31 · diff ↗ ·
added 2 exports
gintervals.annotate, gintervals.normalize
4.3.11
record
2025-08-25 · diff ↗ ·
added 1 export
gtrack.create_dense
R
R 4.5.0 released · 2025-04-11
unarchivedReturned to CRAN
2025-03-06
4.3.6
record
2025-03-06 · diff ↗ ·
added 2 exports
gdb.create_genome, grevcomp
R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2024-03-15
issues were not corrected in time
4.2.9
record
2024-01-15 · diff ↗
unarchivedReturned to CRAN
2023-12-05

Show 5 earlier eventsHide 5 earlier events

4.2.8
record
2023-12-05 · diff ↗
archivedRemoved from CRAN
2023-09-27
check issues were not corrected in time
4.2.6
record
2023-09-14 · diff ↗
4.2.3
record
2023-09-05
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-09-05
Total releases: 13 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.0.0
Download size: 2.0 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("misha")

Format

Lifshitz, A., Weizmann Institute of Science, Hoichman, M., Tanay, A., & Yaffe, E. (2026). misha: Toolkit for Analysis of Genomic Data (Version 5.11.23) [Computer software]. https://doi.org/10.32614/CRAN.package.misha

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 misha version 5.11.23 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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