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scone

https://github.com/yoseflab/scone

Science Score: 23.0%

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
  • ○
    DOI references
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    7 of 23 committers (30.4%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.6%) to scientific vocabulary

Keywords from Contributors

bioconductor-package gene genomics transcriptomics bioinformatics bioconductor human-cell-atlas u24ca289073 core-package single-cell
Last synced: 11 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: YosefLab
  • Language: R
  • Default Branch: master
  • Size: 36 MB
Statistics
  • Stars: 53
  • Watchers: 35
  • Forks: 11
  • Open Issues: 32
  • Releases: 7
Created over 10 years ago · Last pushed over 1 year ago
Metadata Files
Readme

README.md

SCONE

Lifecycle: stable BioC status R-CMD-check <!-- badges: end -->

Single-Cell Overview of Normalized Expression data

SCONE (Single-Cell Overview of Normalized Expression), a package for single-cell RNA-seq data quality control (QC) and normalization. This data-driven framework uses summaries of expression data to assess the efficacy of normalization workflows.

Install from Bioconductor

We recommend installation of the package via bioconductor.

{r} if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("scone")

Install from Github

Usually not recommended. To download the development version of the package, use

{r} BiocManager::install("YosefLab/scone")

Install for R 3.3

You can download the latest release of SCONE for R 3.3 here. This is useful only for reproducing old results.

Owner

  • Name: Yosef Lab
  • Login: YosefLab
  • Kind: organization
  • Location: Israel

Department of Systems Immunology, Weizmann Institute of Science

GitHub Events

Total
  • Watch event: 1
  • Push event: 3
  • Pull request event: 2
  • Fork event: 1
Last Year
  • Watch event: 1
  • Push event: 3
  • Pull request event: 2
  • Fork event: 1

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 331
  • Total Committers: 23
  • Avg Commits per committer: 14.391
  • Development Distribution Score (DDS): 0.547
Past Year
  • Commits: 4
  • Committers: 2
  • Avg Commits per committer: 2.0
  • Development Distribution Score (DDS): 0.5
Top Committers
Name Email Commits
Davide Risso r****e@g****m 150
mbcole m****c@g****m 109
Nitesh Turaga n****a@g****m 14
allonw a****g@e****u 14
Davide Risso d****2@m****u 9
allonwag a****a 9
BRAIN Stat (zen) d****o@b****u 3
Henrik Bengtsson hb@a****g 2
Hervé Pagès h****s@f****g 2
Herve Pages h****s@f****g 2
Michael Cole m****c@M****l 2
J Wokaty j****y@s****u 2
vobencha v****a@g****m 2
vobencha v****n@r****g 2
Michael Cole m****c@a****u 1
Kayla-Morrell k****l@r****g 1
Michael Cole m****e@s****U 1
LiNk-NY m****9@g****m 1
John Blischak j****k@g****m 1
Michael Cole m****e@s****U 1
Martin Morgan m****n@f****g 1
Clarence Mah c****n@g****m 1
lshep l****d@r****g 1
Committer Domains (Top 20 + Academic)
roswellpark.org: 3 fhcrc.org: 2 s121.millennium.berkeley.edu: 1 s124.millennium.berkeley.edu: 1 airbears2-10-142-57-156.airbears2.1918.berkeley.edu: 1 sph.cuny.edu: 1 fredhutch.org: 1 aroma-project.org: 1 berkeley.edu: 1 med.cornell.edu: 1 eecs.berkeley.edu: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 0
  • Total pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: about 6 hours
  • Total issue authors: 0
  • Total pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 1
  • Average time to close issues: N/A
  • Average time to close pull requests: about 6 hours
  • Issue authors: 0
  • Pull request authors: 1
  • Average comments per issue: 0
  • Average comments per pull request: 1.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
Pull Request Authors
  • hpages (1)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

.github/workflows/check-bioc.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • docker/build-push-action v1 composite
  • r-lib/actions/setup-pandoc master composite
  • r-lib/actions/setup-r master composite
DESCRIPTION cran
  • R >= 3.4 depends
  • SummarizedExperiment * depends
  • methods * depends
  • BiocParallel * imports
  • MatrixGenerics * imports
  • RColorBrewer * imports
  • RUVSeq * imports
  • SingleCellExperiment * imports
  • aroma.light * imports
  • boot * imports
  • class * imports
  • cluster * imports
  • compositions * imports
  • diptest * imports
  • edgeR * imports
  • fpc * imports
  • gplots * imports
  • grDevices * imports
  • graphics * imports
  • hexbin * imports
  • limma * imports
  • matrixStats * imports
  • mixtools * imports
  • rARPACK * imports
  • rhdf5 * imports
  • stats * imports
  • utils * imports
  • BiocStyle * suggests
  • DT * suggests
  • NMF * suggests
  • TENxPBMCData * suggests
  • batchtools * suggests
  • doParallel * suggests
  • ggplot2 * suggests
  • kableExtra * suggests
  • knitr * suggests
  • mclust * suggests
  • miniUI * suggests
  • plotly * suggests
  • reshape2 * suggests
  • rmarkdown * suggests
  • scRNAseq * suggests
  • scater * suggests
  • scran * suggests
  • shiny * suggests
  • splatter * suggests
  • testthat * suggests
  • visNetwork * suggests