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SAVER

Single-cell RNA-seq Gene Expression Recovery

https://github.com/mohuangx/saver

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
  • ○
    .zenodo.json file
  • ✓
    DOI references
    Found 2 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    1 of 2 committers (50.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (7.1%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

Single-cell RNA-seq Gene Expression Recovery

Basic Info
  • Host: GitHub
  • Owner: mohuangx
  • License: other
  • Language: R
  • Default Branch: master
  • Size: 3.88 MB
Statistics
  • Stars: 111
  • Watchers: 4
  • Forks: 19
  • Open Issues: 12
  • Releases: 0
Created about 9 years ago · Last pushed over 1 year ago
Metadata Files
Readme

README.md

Travis-CI Build Status CRAN Version

SAVER 1.1.3

SAVER (Single-cell Analysis Via Expression Recovery) implements a regularized regression prediction and empirical Bayes method to recover the true gene expression profile in noisy and sparse single-cell RNA-seq data.

Installation

You can install SAVER from CRAN by running:

R install.packages("SAVER") library(SAVER)

You can also install the most recent updates of SAVER from github with:

```R

install.packages("devtools")

devtools::install_github("mohuangx/SAVER") ```

Reference

For more information about the method, check out the website, tutorial, and paper.

Owner

  • Name: Mo Huang
  • Login: mohuangx
  • Kind: user

Senior Scientist, Biostatistics at Merck

GitHub Events

Total
  • Issues event: 3
  • Watch event: 1
  • Issue comment event: 6
  • Push event: 1
  • Fork event: 1
Last Year
  • Issues event: 3
  • Watch event: 1
  • Issue comment event: 6
  • Push event: 1
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 230
  • Total Committers: 2
  • Avg Commits per committer: 115.0
  • Development Distribution Score (DDS): 0.204
Past Year
  • Commits: 6
  • Committers: 1
  • Avg Commits per committer: 6.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Mo Huang m****g@w****u 183
Mo Huang m****x@g****m 47
Committer Domains (Top 20 + Academic)
wharton.upenn.edu: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time
  • Total issues: 43
  • Total pull requests: 1
  • Average time to close issues: 29 days
  • Average time to close pull requests: 9 days
  • Total issue authors: 36
  • Total pull request authors: 1
  • Average comments per issue: 3.53
  • Average comments per pull request: 2.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 3
  • Pull requests: 0
  • Average time to close issues: 4 days
  • Average time to close pull requests: N/A
  • Issue authors: 3
  • Pull request authors: 0
  • Average comments per issue: 3.33
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • WT215 (3)
  • ravipatel4 (3)
  • inoue0426 (2)
  • zji90 (2)
  • bvieth (2)
  • tilofrei (1)
  • danielgreenwood (1)
  • XueyiDong (1)
  • jamesrhowe (1)
  • gfhtj (1)
  • vertesy (1)
  • FloWuenne (1)
  • MarcelloMalpighi (1)
  • baoyulinn (1)
  • Lumskie (1)
Pull Request Authors
  • bharris12 (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 4
  • Total downloads:
    • cran 349 last-month
  • Total docker downloads: 21,661
  • Total dependent packages: 0
    (may contain duplicates)
  • Total dependent repositories: 2
    (may contain duplicates)
  • Total versions: 32
  • Total maintainers: 1
proxy.golang.org: github.com/mohuangx/SAVER
  • Versions: 14
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 11 months ago
proxy.golang.org: github.com/mohuangx/saver
  • Versions: 14
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Dependent packages count: 5.4%
Average: 5.6%
Dependent repos count: 5.8%
Last synced: 10 months ago
cran.r-project.org: SAVER

Single-Cell RNA-Seq Gene Expression Recovery

  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 2
  • Downloads: 349 Last month
  • Docker Downloads: 21,661
Rankings
Docker downloads count: 0.6%
Stargazers count: 3.8%
Forks count: 4.1%
Average: 16.1%
Dependent repos count: 19.2%
Dependent packages count: 28.7%
Downloads: 40.4%
Maintainers (1)
mohuangx@gmail.com
Last synced: 11 months ago
conda-forge.org: r-saver
  • Versions: 2
  • Dependent Packages: 0
  • Dependent Repositories: 0
Rankings
Stargazers count: 31.4%
Dependent repos count: 34.0%
Forks count: 37.3%
Average: 38.5%
Dependent packages count: 51.2%
Last synced: 11 months ago

Dependencies

DESCRIPTION cran
  • R >= 3.0.1 depends
  • Matrix * imports
  • doParallel * imports
  • foreach * imports
  • glmnet * imports
  • iterators * imports
  • methods * imports
  • knitr * suggests
  • rmarkdown * suggests