r-seuratobject

https://github.com/satijalab/seurat-object

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
3 of 21 committers (14.3%) from academic institutions
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (9.6%) to scientific vocabulary

Keywords from Contributors

human-cell-atlas single-cell-genomics single-cell-rna-seq bioinformatics single-cell atac

Last synced: 10 months ago · JSON representation

Repository

Basic Info

Host: GitHub
Owner: satijalab
License: other
Language: R
Default Branch: main
Homepage: https://satijalab.github.io/seurat-object/
Size: 3.33 MB

Statistics

Stars: 29
Watchers: 7
Forks: 30
Open Issues: 48
Releases: 13

Created almost 6 years ago · Last pushed 10 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%"
)
```

```{r gh.url, echo=FALSE}
ghurl <- function(x) {
  x <- unlist(x = strsplit(x = x, split = ','))
  x <- trimws(x = x)
  x <- grep(pattern = "https://github.com", x = x, value = TRUE)[1]
  return(unname(obj = x))
}
```

```{r cran.cannoncial, echo=FALSE}
cran.cannoncial <- "https://cran.r-project.org/package="
```

```{r load.description, echo=FALSE}
description <- read.dcf(file = "DESCRIPTION")
# Get package name
pkg <- as.vector(x = description[, "Package"])
# Get GitHub URL
github.url <- ghurl(x = description[, "URL"])
# Parse version
pkg.version <- package_version(x = description[1, 'Version'])
stage <- if (pkg.version >= package_version(x = "1.0.0")) {
  "stable"
} else if (pkg.version >= package_version(x = "0.1.0")) {
  "maturing"
} else {
  "experimental"
}
color <- c("experimental" = "orange", "maturing" = "blue", "stable" = "brightgreen")[stage]
```

# SeuratObject


[![Lifecycle](https://img.shields.io/badge/lifecycle-`r stage`-`r color`.svg)](`r github.url`)
[![CRAN/METACRAN](https://img.shields.io/cran/v/`r pkg`)](`r paste0(cran.cannoncial, pkg)`)
[![dependencies](https://tinyverse.netlify.com/badge/`r pkg`)](`r paste0(cran.cannoncial, pkg)`)
[![Downloads](https://cranlogs.r-pkg.org/badges/`r pkg`?color=brightgreen)](`r paste0(cran.cannoncial, pkg)`)


```{r description, echo=FALSE, results='asis'}
cat(gsub(pattern = '\n', replacement = ' ', x = description[, "Description"]))
```

## Installation

`r pkg` is available on CRAN

```r
install.packages("SeuratObject")
```

Owner

Name: satijalab
Login: satijalab
Kind: organization

Website: https://satijalab.org
Twitter: satijalab
Repositories: 12
Profile: https://github.com/satijalab

GitHub Events

Total

Create event: 38
Release event: 2
Issues event: 14
Watch event: 6
Delete event: 36
Issue comment event: 54
Push event: 82
Gollum event: 13
Pull request review comment event: 11
Pull request review event: 21
Pull request event: 56
Fork event: 7

Last Year

Create event: 38
Release event: 2
Issues event: 14
Watch event: 6
Delete event: 36
Issue comment event: 54
Push event: 82
Gollum event: 13
Pull request review comment event: 11
Pull request review event: 21
Pull request event: 56
Fork event: 7

Committers

Last synced: about 1 year ago

All Time

Total Commits: 1,158
Total Committers: 21
Avg Commits per committer: 55.143
Development Distribution Score (DDS): 0.484

Past Year

Commits: 137
Committers: 9
Avg Commits per committer: 15.222
Development Distribution Score (DDS): 0.124

Top Committers

Name	Email	Commits
Paul Hoffman	m****e	598
yuhanH	y**0@n**u	186
David Collins	d**s@n**g	142
Gesmira	g**a@g**m	124
AustinHartman	h**9@g**m	34
zskylarli	z**6@c**u	26
timoast	4****t	15
mhkowalski	m**i@g**m	8
Aaron Wolen	a**n@w**m	4
mischko	m**m@m**g	3
maxim-h	m**v@g**m	3
Saket Choudhary	s**c@g**m	3
Paul Hoffman	p**l@a**g	2
Longda	l**5@g**m	2
Miles Smith	m**h@g**m	2
Diego Diez	d**z@g**m	1
bbimber	b**r@g**m	1
neanderthalensis	7****s	1
rsatija	r**a@n**g	1
Longda Jiang	l**g@n**g	1
samuel-marsh	s**h@c**u	1

Committer Domains (Top 20 + Academic)

nygenome.org: 3 childrens.harvard.edu: 1 airybook.nygenome.org: 1 mailbox.org: 1 wolen.com: 1 columbia.edu: 1 nyu.edu: 1

Issues and Pull Requests

Last synced: 10 months ago

All Time

Total issues: 36
Total pull requests: 77
Average time to close issues: 3 months
Average time to close pull requests: about 2 months
Total issue authors: 33
Total pull request authors: 18
Average comments per issue: 1.97
Average comments per pull request: 0.69
Merged pull requests: 55
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 13
Pull requests: 48
Average time to close issues: about 1 month
Average time to close pull requests: about 1 month
Issue authors: 13
Pull request authors: 11
Average comments per issue: 0.62
Average comments per pull request: 0.6
Merged pull requests: 33
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

vertesy (4)
yerahko (1)
moutazhelal (1)
eunksung (1)
Dazcam (1)
aditisk (1)
nixstix (1)
moi-taiga (1)
adam-cornwell (1)
bbimber (1)
swvanderlaan (1)
Ruba-Mahmoud (1)
PanSX-Dr (1)
jzhou54 (1)
spaette (1)

Pull Request Authors

dcollins15 (38)
mojaveazure (20)
Gesmira (5)
cyrillustan (5)
longmanz (4)
maxim-h (4)
samuel-marsh (4)
mhkowalski (3)
mihem (2)
neanderthalensis (2)
rsatija (2)
mauriziopaul (2)
zskylarli (2)
ddiez (2)
spaette (2)

Top Labels

Issue Labels

Pull Request Labels

enhancement (4)

Packages

Total packages: 2
Total downloads:
- cran 43,785 last-month
Total docker downloads: 151,350

Total dependent packages: 19
(may contain duplicates)
Total dependent repositories: 90
(may contain duplicates)
Total versions: 24
Total maintainers: 1

cran.r-project.org: SeuratObject

Data Structures for Single Cell Data

Homepage: https://satijalab.github.io/seurat-object/
Documentation: http://cran.r-project.org/web/packages/SeuratObject/SeuratObject.pdf
License: MIT + file LICENSE
Latest release: 5.2.0
published 10 months ago

Versions: 15
Dependent Packages: 18
Dependent Repositories: 86
Downloads: 43,785 Last month
Docker Downloads: 151,350

Rankings

Downloads: 1.7%

Dependent repos count: 2.5%

Dependent packages count: 4.0%

Forks count: 4.3%

Average: 7.7%

Stargazers count: 15.8%

Docker downloads count: 17.6%

Maintainers (1)

seurat@nygenome.org

Last synced: 10 months ago

conda-forge.org: r-seuratobject

Homepage: https://satijalab.github.io/seurat-object/
License: MIT
Latest release: 4.1.3
published over 3 years ago

Versions: 9
Dependent Packages: 1
Dependent Repositories: 4

Rankings

Dependent repos count: 16.1%

Average: 22.5%

Dependent packages count: 29.0%

Last synced: 10 months ago

Dependencies

DESCRIPTION cran

R >= 4.0.0 depends
Matrix >= 1.3.3 imports
Rcpp >= 1.0.5 imports
future * imports
future.apply * imports
grDevices * imports
grid * imports
methods * imports
progressr * imports
rgeos * imports
rlang >= 0.4.7 imports
sp * imports
stats * imports
tools * imports
utils * imports
ggplot2 * suggests
testthat * suggests

.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

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

r-seuratobject

Science Score: 36.0%

Keywords from Contributors

Repository

Basic Info

Statistics

Metadata Files

README.Rmd

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

cran.r-project.org: SeuratObject

Rankings

Maintainers (1)

conda-forge.org: r-seuratobject

Rankings

Dependencies