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CHETAH

scRNA-seq cell type identification

https://github.com/jdekanter/chetah

Science Score: 13.0%

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    Found 1 DOI reference(s) in README
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    Low similarity (8.3%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

scRNA-seq cell type identification

Basic Info
  • Host: GitHub
  • Owner: jdekanter
  • License: agpl-3.0
  • Language: R
  • Default Branch: master
  • Size: 3.5 MB
Statistics
  • Stars: 43
  • Watchers: 3
  • Forks: 10
  • Open Issues: 4
  • Releases: 0
Created over 7 years ago · Last pushed almost 7 years ago
Metadata Files
Readme License

README.md

CHETAH: a selective, hierarchical cell type identification method for single-cell RNA sequencing

CHETAH is an R package for cell type identification of single-cell RNA-sequencing (scRNA-seq) data. Cell types are assigned by correlating the input data to a reference in a hierarchical manner. CHETAH is built to work with scRNA-seq references, but will also work (with limited capabilities) with RNA-seq or micro-array reference datasets.

The article describing CHETAH can be found at: Nucleic Acids Research.

CHETAH is now part of Bioconductor.

CHETAH can be installed by running: ```{r echo=TRUE, eval=FALSE} if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("CHETAH") ```

To get to know the basics of the CHETAH pacakge, please look at the vignette; {r echo=TRUE, eval=FALSE} vignette("CHETAH_introduction")

At a glance: to run chetah on an input count matrix input_counts with t-SNE coordinates in input_tsne, and a reference count matrix ref_counts with celltypes vector ref_ct, run:

```{r glance, echo=TRUE, eval=FALSE}

Make SingleCellExperiments

reference <- SingleCellExperiment(assays = list(counts = refcounts), colData = DataFrame(celltypes = refct))

input <- SingleCellExperiment(assays = list(counts = inputcounts), reducedDims = SimpleList(TSNE = inputtsne))

Run CHETAH

input <- CHETAHclassifier(input = input, ref_cells = reference)

Plot the classification

PlotCHETAH(input)

Extract celltypes:

celltypes <- input$celltype_CHETAH ```

Owner

  • Name: J. K. de Kanter
  • Login: jdekanter
  • Kind: user
  • Location: The Netherlands
  • Company: Princes Máxima Center for Pedriatic Oncology

GitHub Events

Total
  • Issues event: 1
  • Watch event: 3
  • Fork event: 1
Last Year
  • Issues event: 1
  • Watch event: 3
  • Fork event: 1

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 42
  • Total Committers: 3
  • Avg Commits per committer: 14.0
  • Development Distribution Score (DDS): 0.071
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
jdekanter j****r@s****l 39
Nitesh Turaga n****a@g****m 2
J. K. de Kanter 3****r 1
Committer Domains (Top 20 + Academic)
students.uu.nl: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 1
  • Total pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Total issue authors: 1
  • Total pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 1
  • Pull request authors: 0
  • Average comments per issue: 0.0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
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Top Authors
Issue Authors
  • shraddhapai (1)
Pull Request Authors
Top Labels
Issue Labels
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Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 14,375 total
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: CHETAH

Fast and accurate scRNA-seq cell type identification

  • Versions: 5
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 14,375 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 20.7%
Downloads: 62.1%
Maintainers (1)
jurriandekanter@gmail.com
Last synced: 12 months ago