misha

5.6.6

Toolkit for Analysis of Genomic Data

0packages depend

2.9Kdownloads / year

40.9%test coverage

9/10checks pass

Overview

About

Maintained by Aviezer LifshitzFirst published 2023-09-0512 releasesCRAN page ↗GitHub ↗

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.

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.

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).

Health

CRAN checks

1NOTE9OK

Failing flavors

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

Slowest check: 16.9 min · r-devel-linux-x86_64-fedora-clang

Code health

Yes

Tests · ratio 2.31

40.9%

Coverage · measured lines

99%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
9 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
10 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-06-08
9 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-07
9 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-11
10 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Show 5 earlier snapshots

WARNING2026-05-10
9 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE
OK2026-05-02
10 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-10
5 OK · 6 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
4 OK · 6 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
NOTE2026-03-10
9 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 182 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 85%
Documented parameters: 95%
Return-value docs: 99%
References docs: 0%

Downloads

2.9K

CRAN downloads in the past year

Rank #17,458 · ~8/day · ~242/mo

Releases R versions

Daily download trend is not available in this view yet.

11630 days

62090 days

2.9K1 year

Compare downloads with other packages →

Also on482 r2u4 autocran9.5K bioconda

Repository

GitHub ↗ tanaylab/misha

4Stars

2Forks

1Open issues

3Open PRs

51Releases

806Commits

3Contributors

genomic-data-analysis

806 commits · Last activity 2026-07-27 · 0% stars, 30d

Stars over time

2022-11-02 · 42026-07-07 · 4

Repository practices

Upstream repositoryBeta

4 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/tanaylab/misha on 2026-08-02.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

16 external dependencies (excludes base and recommended)

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

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (5)

Maintainer (1)

Aviezer Lifshitz

Author, Maintainer

Authors (4)

Author, Maintainer

Author

Author

Author

Weizmann Institute of Science

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
5.6.6Latest
2026-03-20 · current release · diff ↗
5.4.5
2026-02-20 · diff ↗
5.4.0
2026-01-27 · diff ↗
5.3.2
2025-12-14 · diff ↗
5.3.1
2025-12-10 · diff ↗
4.3.12
2025-08-31 · diff ↗
4.3.11
2025-08-25 · diff ↗
R
R 4.5.0 released · 2025-04-11
4.3.6
2025-03-06 · diff ↗
unarchivedReturned to CRAN
2025-03-06
R
R 4.4.0 released · 2024-04-24
archivedRemoved from CRAN
2024-03-15
issues were not corrected in time
4.2.9
2024-01-15 · diff ↗
4.2.8
2023-12-05 · diff ↗
unarchivedReturned to CRAN
2023-12-05

Show 4 earlier events

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

Package metadata

First published: 2023-09-05
Total releases: 12 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.0.0
Download size: 1.4 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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