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valr

Genome Interval Arithmetic in R

https://github.com/rnabioco/valr

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
    2 of 10 committers (20.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.6%) to scientific vocabulary

Keywords

bedtools genome interval-arithmetic

Keywords from Contributors

single-cell-rna-seq assign-identities clusters marker-genes rna-seq bioconductor-package rna-seq-analysis single-cell-analysis
Last synced: 6 months ago · JSON representation

Repository

Genome Interval Arithmetic in R

Basic Info
Statistics
  • Stars: 93
  • Watchers: 7
  • Forks: 25
  • Open Issues: 4
  • Releases: 26
Topics
bedtools genome interval-arithmetic
Created about 10 years ago · Last pushed 6 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct

README.Rmd 

---
output: github_document
---

```{r, echo = FALSE, message = FALSE}
knitr::opts_chunk$set(
  fig.align = "center",
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-"
)
```

# valr 


[![R-CMD-check](https://github.com/rnabioco/valr/actions/workflows/check-standard.yaml/badge.svg)](https://github.com/rnabioco/valr/actions/workflows/check-standard.yaml)
[![codecov](https://codecov.io/github/rnabioco/valr/graph/badge.svg)](https://app.codecov.io/github/rnabioco/valr)
[![](https://www.r-pkg.org/badges/version/valr)](https://CRAN.R-project.org/package=valr)


valr provides tools to read and manipulate genome intervals and signals, similar to the [BEDtools](https://bedtools.readthedocs.io/en/latest/) suite. 

## Installation

::: .pkgdown-release
```{r, eval = FALSE}
# Install released version from CRAN
install.packages("valr")
```
:::

::: .pkgdown-devel
```{r, eval = FALSE}
# Install development version from GitHub
# install.packages("pak")
pak::pak("rnabioco/valr")
```
:::

## valr Example

Functions in valr have similar names to their BEDtools counterparts, and so will be familiar to users coming from the BEDtools suite. Unlike other tools that wrap BEDtools and write temporary files to disk, valr tools run natively in memory. Similar to [pybedtools](https://daler.github.io/pybedtools/#why-pybedtools), valr has a terse syntax:

```{r syntax_demo, message = FALSE}
library(valr)
library(dplyr)

snps <- read_bed(valr_example("hg19.snps147.chr22.bed.gz"))
genes <- read_bed(valr_example("genes.hg19.chr22.bed.gz"))

# find snps in intergenic regions
intergenic <- bed_subtract(snps, genes)
# find distance from intergenic snps to nearest gene
nearby <- bed_closest(intergenic, genes)

nearby |>
  select(starts_with("name"), .overlap, .dist) |>
  filter(abs(.dist) < 5000)
```

Owner

  • Name: RNA Bioscience Initiative (RBI)
  • Login: rnabioco
  • Kind: organization
  • Email: jay.hesselberth@cuanschutz.edu
  • Location: University of Colorado School of Medicine

The RNA Bioscience Initiative Informatics Fellows program

GitHub Events

Total
  • Issues event: 16
  • Watch event: 4
  • Delete event: 7
  • Issue comment event: 27
  • Push event: 73
  • Pull request review comment event: 2
  • Pull request review event: 3
  • Pull request event: 17
  • Fork event: 1
  • Create event: 9
Last Year
  • Issues event: 16
  • Watch event: 4
  • Delete event: 7
  • Issue comment event: 27
  • Push event: 73
  • Pull request review comment event: 2
  • Pull request review event: 3
  • Pull request event: 17
  • Fork event: 1
  • Create event: 9

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 914
  • Total Committers: 10
  • Avg Commits per committer: 91.4
  • Development Distribution Score (DDS): 0.184
Past Year
  • Commits: 32
  • Committers: 3
  • Avg Commits per committer: 10.667
  • Development Distribution Score (DDS): 0.344
Top Committers
Name Email Commits
Jay Hesselberth j****h@g****m 746
Kent Riemondy k****y@g****m 124
kriemo k****o 22
sheridar r****n@u****u 7
Jay Hesselberth j****h@c****u 6
Ray r****s@g****m 3
agillen a****n@g****m 2
Jim Hester j****r@g****m 2
Ryan Mackie m****5@g****m 1
Henry Miller 4****1 1
Committer Domains (Top 20 + Academic)
cuanschutz.edu: 1 ucdenver.edu: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 71
  • Total pull requests: 67
  • Average time to close issues: 6 months
  • Average time to close pull requests: 21 days
  • Total issue authors: 17
  • Total pull request authors: 9
  • Average comments per issue: 2.08
  • Average comments per pull request: 0.75
  • Merged pull requests: 52
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 9
  • Pull requests: 16
  • Average time to close issues: 8 days
  • Average time to close pull requests: 2 days
  • Issue authors: 4
  • Pull request authors: 2
  • Average comments per issue: 3.33
  • Average comments per pull request: 0.19
  • Merged pull requests: 9
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • jayhesselberth (38)
  • kriemo (10)
  • raysinensis (5)
  • kcamnairb (3)
  • sheridar (2)
  • sigven (2)
  • millerh1 (1)
  • BiodeB (1)
  • krlmlr (1)
  • canholyavkin (1)
  • nemartins (1)
  • frequena (1)
  • kbauerm (1)
  • CeesBM (1)
  • ItokawaK (1)
Pull Request Authors
  • jayhesselberth (34)
  • kriemo (25)
  • raysinensis (5)
  • jimhester (2)
  • teunbrand (2)
  • romainfrancois (1)
  • millerh1 (1)
  • sheridar (1)
  • agillen (1)
Top Labels
Issue Labels
bug :bug: (4) cpp (1) reprex (1)
Pull Request Labels

Packages

  • Total packages: 3
  • Total downloads:
    • cran 1,169 last-month
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 4
    (may contain duplicates)
  • Total versions: 52
  • Total maintainers: 1
proxy.golang.org: github.com/rnabioco/valr
  • Versions: 26
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.5%
Average: 5.7%
Dependent repos count: 5.9%
Last synced: 6 months ago
cran.r-project.org: valr

Genome Interval Arithmetic

  • Versions: 25
  • Dependent Packages: 0
  • Dependent Repositories: 4
  • Downloads: 1,169 Last month
Rankings
Forks count: 3.2%
Stargazers count: 4.4%
Average: 13.9%
Dependent repos count: 14.5%
Downloads: 18.5%
Dependent packages count: 28.7%
Maintainers (1)
kent.riemondy@gmail.com
Last synced: 6 months ago
conda-forge.org: r-valr
  • Versions: 1
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Forks count: 30.8%
Stargazers count: 32.7%
Dependent repos count: 34.0%
Average: 37.2%
Dependent packages count: 51.2%
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.1.2 depends
  • Rcpp >= 1.0.0 imports
  • broom * imports
  • dplyr >= 0.8.0 imports
  • ggplot2 * imports
  • readr * imports
  • rlang * imports
  • rtracklayer * imports
  • stringr * imports
  • tibble >= 1.4.2 imports
  • DBI * suggests
  • DT * suggests
  • GenomicRanges * suggests
  • IRanges * suggests
  • RMariaDB * suggests
  • S4Vectors * suggests
  • bench * suggests
  • covr * suggests
  • cowplot * suggests
  • curl * suggests
  • dbplyr * suggests
  • devtools * suggests
  • knitr * suggests
  • purrr * suggests
  • rmarkdown * suggests
  • testthat * suggests
  • tidyr * suggests
.github/workflows/check-standard.yaml actions
  • actions/checkout v2 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 4.1.4 composite
  • actions/checkout 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/pr-commands.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/pr-fetch v2 composite
  • r-lib/actions/pr-push v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite
.github/workflows/test-coverage.yaml actions
  • actions/checkout v2 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite