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clustermole

Unbiased single-cell transcriptomic data cell type identification

https://github.com/igordot/clustermole

Science Score: 44.0%

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

  • ✓
    CITATION.cff file
    Found 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
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (5.3%) to scientific vocabulary

Keywords

cell-type cell-type-annotation cell-type-classification cell-type-identification cell-type-matching gene-expression-signatures scrna-seq single-cell
Last synced: 6 months ago · JSON representation ·

Repository

Unbiased single-cell transcriptomic data cell type identification

Basic Info
Statistics
  • Stars: 13
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 4
Topics
cell-type cell-type-annotation cell-type-classification cell-type-identification cell-type-matching gene-expression-signatures scrna-seq single-cell
Created over 6 years ago · Last pushed almost 2 years ago
Metadata Files
Readme Changelog License Citation

README.md

clustermole: exploratory scRNA-seq cell type analysis

The clustermole R package (available on CRAN) provides methods to query cell identity markers sourced from a variety of databases. It includes three primary features:

  • a meta-database of human and mouse markers for thousands of cell types
  • cell type prediction based on a set of marker genes
  • cell type prediction based on a table of expression values

Check the documentation website for more information.

Owner

  • Name: igor
  • Login: igordot
  • Kind: user
  • Location: New York, NY, USA
  • Company: New York University School of Medicine

Citation (CITATION.cff) 

# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "clustermole" in publications use:'
type: software
license: MIT
title: 'clustermole: Unbiased Single-Cell Transcriptomic Data Cell Type Identification'
version: 1.1.1
abstract: Assignment of cell type labels to single-cell RNA sequencing (scRNA-seq)
  clusters is often a time-consuming process that involves manual inspection of the
  cluster marker genes complemented with a detailed literature search. This is especially
  challenging when unexpected or poorly described populations are present. The clustermole
  R package provides methods to query thousands of human and mouse cell identity markers
  sourced from a variety of databases.
authors:
- family-names: Dolgalev
  given-names: Igor
  email: igor.dolgalev@nyumc.org
  orcid: https://orcid.org/0000-0003-4451-126X
repository: https://CRAN.R-project.org/package=clustermole
repository-code: https://github.com/igordot/clustermole
url: https://igordot.github.io/clustermole/
contact:
- family-names: Dolgalev
  given-names: Igor
  email: igor.dolgalev@nyumc.org
  orcid: https://orcid.org/0000-0003-4451-126X

GitHub Events

Total
  • Watch event: 1
Last Year
  • Watch event: 1

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 35
  • Total Committers: 2
  • Avg Commits per committer: 17.5
  • Development Distribution Score (DDS): 0.314
Top Committers
Name Email Commits
igor 6****t@u****m 24
igor i****t@u****m 11

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 4
  • Total pull requests: 0
  • Average time to close issues: 2 months
  • Average time to close pull requests: N/A
  • Total issue authors: 3
  • Total pull request authors: 0
  • Average comments per issue: 1.5
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • bashhike (1)
  • jcorn427 (1)
  • sesemina (1)
Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • cran 436 last-month
  • Total docker downloads: 21,638
  • Total dependent packages: 0
  • Total dependent repositories: 1
  • Total versions: 4
  • Total maintainers: 1
cran.r-project.org: clustermole

Unbiased Single-Cell Transcriptomic Data Cell Type Identification

  • Versions: 4
  • Dependent Packages: 0
  • Dependent Repositories: 1
  • Downloads: 436 Last month
  • Docker Downloads: 21,638
Rankings
Stargazers count: 17.7%
Dependent repos count: 24.7%
Average: 25.1%
Downloads: 26.1%
Forks count: 28.4%
Dependent packages count: 28.5%
Maintainers (1)
igor.dolgalev@nyumc.org
Last synced: 6 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.6 depends
  • GSEABase * imports
  • GSVA >= 1.26.0 imports
  • dplyr * imports
  • magrittr * imports
  • methods * imports
  • rlang >= 0.1.2 imports
  • singscore * imports
  • tibble * imports
  • tidyr * imports
  • utils * imports
  • covr * suggests
  • knitr * suggests
  • prettydoc * suggests
  • rmarkdown * suggests
  • roxygen2 * suggests
  • testthat >= 2.1.0 suggests
.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/test-coverage.yaml actions
  • actions/checkout v3 composite
  • actions/upload-artifact v3 composite
  • r-lib/actions/setup-r v2 composite
  • r-lib/actions/setup-r-dependencies v2 composite