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misha

Genomic data analysis suite

https://github.com/tanaylab/misha

Science Score: 36.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 3 committers (33.3%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.6%) to scientific vocabulary

Keywords

genomic-data-analysis
Last synced: 9 months ago · JSON representation

Repository

Genomic data analysis suite

Basic Info
Statistics
  • Stars: 4
  • Watchers: 2
  • Forks: 1
  • Open Issues: 2
  • Releases: 11
Topics
genomic-data-analysis
Created almost 7 years ago · Last pushed 9 months ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.path = "man/figures/README-",
    out.width = "100%"
)
```

# misha


[![CRAN status](https://www.r-pkg.org/badges/version/misha)](https://CRAN.R-project.org/package=misha)
[![R-CMD-check](https://github.com/tanaylab/misha/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/tanaylab/misha/actions/workflows/R-CMD-check.yaml)


The `misha` package is a toolkit for analysis of genomic data. it implements an efficient data structure for storing genomic data, and provides a set of functions for data extraction, manipulation and analysis.

## Installation

You can install the released version of misha from [CRAN](https://CRAN.R-project.org) with:

```{r, eval=FALSE}
install.packages("misha")
```

And the development version from GitHub with:

```{r, eval=FALSE}
remotes::install_github("tanaylab/misha")
```

## Usage 

See the [Genomes](https://tanaylab.github.io/misha/articles/Genomes.html) vignette for instructions on how to create a misha database for common genomes.

See the [user manual](https://tanaylab.github.io/misha/articles/Manual.html) for more usage details.

#### Running scripts from old versions of misha (< 4.2.0)

Starting in `misha` 4.2.0, the package no longer stores global variables such as `ALLGENOME` or `GROOT`. Instead, these variables are stored in a special environment called `.misha`. This means that scripts written for older versions of `misha` will no longer work. To run such scripts, either add a prefix of `.misha$` to all those variables (`.misha$ALLGENOME` instead of `ALLGENOME`), or run the following command before running the script:

```{r, eval=FALSE}
ALLGENOME <<- .misha$ALLGENOME
GROOT <<- .misha$GROOT
ALLGENOME <<- .misha$ALLGENOME
GINTERVID <<- .misha$GINTERVID
GITERATOR.INTERVALS <<- .misha$GITERATOR.INTERVALS
GROOT <<- .misha$GROOT
GWD <<- .misha$GWD
GTRACKS <<- .misha$GTRACKS
```

Owner

  • Name: tanaylab
  • Login: tanaylab
  • Kind: organization

GitHub Events

Total
  • Create event: 21
  • Release event: 7
  • Issues event: 4
  • Delete event: 13
  • Issue comment event: 5
  • Push event: 103
  • Pull request review comment event: 3
  • Pull request review event: 3
  • Pull request event: 19
Last Year
  • Create event: 21
  • Release event: 7
  • Issues event: 4
  • Delete event: 13
  • Issue comment event: 5
  • Push event: 103
  • Pull request review comment event: 3
  • Pull request review event: 3
  • Pull request event: 19

Committers

Last synced: 11 months ago

All Time
  • Total Commits: 187
  • Total Committers: 3
  • Avg Commits per committer: 62.333
  • Development Distribution Score (DDS): 0.048
Past Year
  • Commits: 49
  • Committers: 1
  • Avg Commits per committer: 49.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
aviezerl a****z@w****l 178
Misha Hoichman m****a@h****m 7
hoichman 5****n 2
Committer Domains (Top 20 + Academic)
hoichman.com: 1 weizmann.ac.il: 1

Issues and Pull Requests

Last synced: 9 months ago

All Time
  • Total issues: 13
  • Total pull requests: 29
  • Average time to close issues: 11 months
  • Average time to close pull requests: about 12 hours
  • Total issue authors: 7
  • Total pull request authors: 2
  • Average comments per issue: 1.46
  • Average comments per pull request: 0.17
  • Merged pull requests: 23
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 22
  • Average time to close issues: 2 months
  • Average time to close pull requests: about 7 hours
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.09
  • Merged pull requests: 17
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jiangpuxuan (3)
  • yonatans2 (3)
  • aviezerl (3)
  • srcoulombe (1)
  • ofirr (1)
  • dpryan79 (1)
  • jmarshall (1)
Pull Request Authors
  • aviezerl (28)
  • jmarshall (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 186 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 5
  • Total versions: 7
  • Total maintainers: 1
cran.r-project.org: misha

Toolkit for Analysis of Genomic Data

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 5
  • Downloads: 186 Last month
Rankings
Dependent repos count: 13.0%
Forks count: 21.0%
Stargazers count: 23.6%
Dependent packages count: 28.7%
Average: 34.4%
Downloads: 85.7%
Maintainers (1)
aviezer.lifshitz@weizmann.ac.il
Last synced: 9 months ago

Dependencies

DESCRIPTION cran
  • utils * depends
.github/workflows/R-CMD-check.yaml actions
  • actions/checkout v3 composite
  • r-lib/actions/check-r-package v2 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/pkgdown.yaml actions
  • JamesIves/github-pages-deploy-action v4.4.1 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/style.yaml actions
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite