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nebulosa

R package to visualize gene expression data based on weighted kernel density estimation

https://github.com/powellgenomicslab/nebulosa

Science Score: 13.0%

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
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    DOI references
  • ○
    Academic publication links
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    Committers with academic emails
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    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.4%) to scientific vocabulary

Keywords

single-cell single-cell-analysis single-cell-multiomics single-cell-rna-seq
Last synced: 6 months ago · JSON representation

Repository

R package to visualize gene expression data based on weighted kernel density estimation

Basic Info
  • Host: GitHub
  • Owner: powellgenomicslab
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 264 KB
Statistics
  • Stars: 103
  • Watchers: 3
  • Forks: 12
  • Open Issues: 26
  • Releases: 1
Topics
single-cell single-cell-analysis single-cell-multiomics single-cell-rna-seq
Created over 5 years ago · Last pushed almost 2 years ago
Metadata Files
Readme

README.md

Nebulosa

Build Status https://www.tidyverse.org/lifecycle/#maturing

Motivation

Due to the sparsity observed in single-cell data (e.g. RNA-seq, ATAC-seq), the visualization of cell features (e.g. gene, peak) is frequently affected and unclear, especially when it is overlaid with clustering to annotate cell types. Nebulosa is an R package to visualize data from single cells based on kernel density estimation. It aims to recover the signal from dropped-out features by incorporating the similarity between cells allowing a “convolution” of the cell features.

Installation

Nebulosa is available on Bioconductor and can be installed as follows:

```R if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("Nebulosa") ```

See Nebulosa for more details.

You can install the developing version of Nebulosa from github via devtools:

R devtools::install_github("powellgenomicslab/Nebulosa")

Vignettes

Nebulosa can use Seurat and SingleCellExperiment objects. See the corresponding vignette:

Owner

  • Name: Single Cell Computational Genomics
  • Login: powellgenomicslab
  • Kind: organization
  • Location: Australia

GitHub Events

Total
  • Issues event: 2
  • Watch event: 20
  • Issue comment event: 4
  • Pull request event: 1
  • Fork event: 3
Last Year
  • Issues event: 2
  • Watch event: 20
  • Issue comment event: 4
  • Pull request event: 1
  • Fork event: 3

Committers

Last synced: over 1 year ago

All Time
  • Total Commits: 104
  • Total Committers: 5
  • Avg Commits per committer: 20.8
  • Development Distribution Score (DDS): 0.067
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
joseah a****e@g****m 97
Gökçen Eraslan g****n@g****m 2
Nitesh Turaga n****a@g****m 2
Paul Hoffman m****e 2
Katherine Beigel 1****k 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 26
  • Total pull requests: 7
  • Average time to close issues: 1 day
  • Average time to close pull requests: 2 days
  • Total issue authors: 26
  • Total pull request authors: 5
  • Average comments per issue: 1.62
  • Average comments per pull request: 0.57
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 2
  • Pull requests: 2
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 2
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ganpha (1)
  • MelissaSaichi (1)
  • yuGithuuub (1)
  • michaelcvermeulen (1)
  • ftencaten (1)
  • Noralii (1)
  • levinhein (1)
  • Xiangruili-seed (1)
  • mhwadsworth91 (1)
  • ghost (1)
  • Hrovatin (1)
  • mmokrejs (1)
  • ttriche (1)
  • honghh2018 (1)
  • denvercal1234GitHub (1)
Pull Request Authors
  • mihem (2)
  • mojaveazure (2)
  • beigelk (2)
  • samuel-marsh (1)
  • gokceneraslan (1)
Top Labels
Issue Labels
question (1) enhancement (1)
Pull Request Labels

Dependencies

DESCRIPTION cran
  • R >= 4.0 depends
  • ggplot2 * depends
  • patchwork * depends
  • Matrix * imports
  • SeuratObject * imports
  • SingleCellExperiment * imports
  • SummarizedExperiment * imports
  • ks * imports
  • methods * imports
  • stats * imports
  • BiocFileCache * suggests
  • BiocStyle * suggests
  • DropletUtils * suggests
  • Seurat * suggests
  • covr * suggests
  • igraph * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • scater * suggests
  • scran * suggests
  • testthat * suggests