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scmap

A tool for unsupervised projection of single cell RNA-seq data

https://github.com/hemberg-lab/scmap

Science Score: 20.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: nature.com
  • ✓
    Committers with academic emails
    2 of 10 committers (20.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.2%) to scientific vocabulary

Keywords

bioconductor-package human-cell-atlas projection-mapping r single-cell-rna-seq

Keywords from Contributors

transcriptomics genomics gene single-cell bioinformatics rna-seq gene-expression proteomics taxonomy mass-spectrometry
Last synced: 11 months ago · JSON representation

Repository

A tool for unsupervised projection of single cell RNA-seq data

Basic Info
Statistics
  • Stars: 95
  • Watchers: 11
  • Forks: 11
  • Open Issues: 21
  • Releases: 0
Topics
bioconductor-package human-cell-atlas projection-mapping r single-cell-rna-seq
Created over 9 years ago · Last pushed over 5 years ago
Metadata Files
Readme License

README.md

scmap - A tool for unsupervised projection of single cell RNA-seq data

Single-cell RNA-seq (scRNA-seq) is widely used to investigate the composition of complex tissues since the technology allows researchers to define cell-types using unsupervised clustering of the transcriptome. However, due to differences in experimental methods and computational analyses, it is often challenging to directly compare the cells identified in two different experiments. Here, we present scmap, a method for projecting cells from a scRNA-seq experiment on to the cell-types identified in a different experiment.

Cloud-based scmap

Instructions on how to set it up on your own Cloud are available here.

Questions

Q: How to install/run scmap?
A: Please follow instruction on Bioconductor page. If there are any problems you can install scmap from GitHub: ```

run this in your R session

install.packages("devtools") devtools::install_github("hemberg-lab/scmap") ```

Q: Where can I report bugs, comments, issues or suggestions?
A: Please use this page.

Q: Where can I ask questions about scmap?
A: Please use this page.

Q: Is scmap published?
A: Yes, it is published in Nature Methods.

Q: What is scmap licence?
A: GPL-3

Owner

  • Name: Hemberg Lab
  • Login: hemberg-lab
  • Kind: organization
  • Location: United States of America

GitHub Events

Total
  • Issues event: 1
  • Watch event: 7
Last Year
  • Issues event: 1
  • Watch event: 7

Committers

Last synced: about 1 year ago

All Time
  • Total Commits: 117
  • Total Committers: 10
  • Avg Commits per committer: 11.7
  • Development Distribution Score (DDS): 0.265
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Vladimir Kiselev v****v@g****m 86
wikiselev v****6@s****k 13
Nitesh Turaga n****a@g****m 4
Andrew Yiu a****2@l****m 4
vobencha v****a@g****m 2
Hervé Pagès h****s@f****g 2
vobencha v****n@r****g 2
Andrew Yiu a****2@l****k 2
Kayla-Morrell k****l@r****g 1
Martin Morgan m****n@f****g 1
Committer Domains (Top 20 + Academic)
roswellpark.org: 2 fhcrc.org: 1 loan105946.internal.sanger.ac.uk: 1 fredhutch.org: 1 loan105946.hinxtonit.com: 1 sanger.ac.uk: 1

Issues and Pull Requests

Last synced: about 1 year ago

All Time
  • Total issues: 39
  • Total pull requests: 2
  • Average time to close issues: 28 days
  • Average time to close pull requests: 6 days
  • Total issue authors: 31
  • Total pull request authors: 2
  • Average comments per issue: 2.62
  • Average comments per pull request: 0.5
  • Merged pull requests: 1
  • 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
View more stats
Top Authors
Issue Authors
  • CodeInTheSkies (5)
  • FionaMoon (2)
  • Kevis9 (2)
  • mxposed (2)
  • aopisco (2)
  • Jiam1ng (1)
  • ivanaarellano (1)
  • dat4git (1)
  • jsonProgram (1)
  • pongslepha (1)
  • atakanekiz (1)
  • finjen (1)
  • Diennguyen8290 (1)
  • liuhao-stark (1)
  • davetang (1)
Pull Request Authors
  • ay2sanger (1)
  • Arlene-1998 (1)
Top Labels
Issue Labels
enhancement (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 37,636 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: scmap

A tool for unsupervised projection of single cell RNA-seq data

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 37,636 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 9.9%
Downloads: 29.8%
Maintainers (1)
vladimir.yu.kiselev@gmail.com
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.4 depends
  • Biobase * imports
  • BiocGenerics * imports
  • Rcpp >= 0.12.12 imports
  • S4Vectors * imports
  • SingleCellExperiment * imports
  • SummarizedExperiment * imports
  • dplyr * imports
  • e1071 * imports
  • ggplot2 * imports
  • googleVis * imports
  • matrixStats * imports
  • methods * imports
  • proxy * imports
  • randomForest * imports
  • reshape2 * imports
  • stats * imports
  • utils * imports
  • knitr * suggests
  • rmarkdown * suggests