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multiMiR

Development repository for the multiMiR database's R API

https://github.com/kechrislab/multimir

Science Score: 10.0%

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
  • ✓
    Committers with academic emails
    2 of 10 committers (20.0%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (11.0%) to scientific vocabulary

Keywords

microrna-sequence r sql

Keywords from Contributors

bioconductor-package genomics gene scrna-seq gene-expression proteomics atac-seq tcga core-services bioconductor
Last synced: 6 months ago · JSON representation

Repository

Development repository for the multiMiR database's R API

Basic Info
  • Host: GitHub
  • Owner: KechrisLab
  • License: other
  • Language: R
  • Default Branch: master
  • Homepage:
  • Size: 568 KB
Statistics
  • Stars: 20
  • Watchers: 5
  • Forks: 3
  • Open Issues: 11
  • Releases: 0
Topics
microrna-sequence r sql
Created about 9 years ago · Last pushed over 1 year ago
Metadata Files
Readme License

README.md

multiMiR

Build Status codecov biocdownloads

inBioc

DB update is available 8/28/24 (Thank you for your patience)

The multiMiR web server hosts a database containing miRNA-target interactions from external databases. The package multiMiR provides functions to communicate with the multiMiR web server and its database.

Note this repository is where active development occurs (think 'nightly' builds). The recommended release and devel versions are available via Bioconductor (as of Bioconductor 3.6).

```{r}

To install multiMiR, use BiocManager::install()

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

Terminology used in package: - sql components: SELECT or FROM or ON or WHERE... etc. (mmsql_components class) - sql features: specific to this DB and the options used to generate meaningful queries (i.e. mirna; conserved; table type: validated, predicted; etc.) - sql: a complete sql statement (mmsql class) - query: table result of sql statement (mmquery class), class includes sql statement and parts.

* Warning * There are issues with merging target IDs from older unmaintained databases. Databases that have been updated more recently (1-2 years) use current versions of annotated IDs. In each update these old target IDs are carried over due to a lack of a reliable method to disambiguate the original ID with current IDs. Please keep this in mind with results from older databases that have not been updated. We continue to look at methods to resolve these ambiguities and improve target agreement between databases. You can use the unique() R function to identify and then remove multiple target genes if needed.

Owner

  • Name: KechrisLab
  • Login: KechrisLab
  • Kind: organization

GitHub Events

Total
  • Issues event: 1
  • Issue comment event: 1
Last Year
  • Issues event: 1
  • Issue comment event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 189
  • Total Committers: 10
  • Avg Commits per committer: 18.9
  • Development Distribution Score (DDS): 0.487
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Matt Mulvahill (MtEvans) m****l@u****u 97
Matt Mulvahill (peregrine) m****l@g****m 61
Spencer Mahaffey S****y@u****u 12
Nitesh Turaga n****a@g****m 6
Matt c****l@c****m 5
vobencha v****a@g****m 2
Hervé Pagès h****s@f****g 2
vobencha v****n@r****g 2
LiNk-NY m****z@r****g 1
LiNk-NY m****9@g****m 1
Committer Domains (Top 20 + Academic)
roswellpark.org: 2 ucdenver.edu: 2 fredhutch.org: 1 charter.com: 1

Issues and Pull Requests

Last synced: 6 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
View more stats
Top Authors
Issue Authors
  • smahaffey (2)
  • karlaarz (1)
  • Eunbi61 (1)
  • beginner984 (1)
  • mattbcvs (1)
  • jeremydavisturak (1)
  • TheMuffinMan563 (1)
  • SergejRuff (1)
  • polya18 (1)
  • JoseCorCab (1)
  • DaniHiam (1)
Pull Request Authors
Top Labels
Issue Labels
bug (6) Database (2) enhancement (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 28,615 total
  • Total dependent packages: 1
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: multiMiR

Integration of multiple microRNA-target databases with their disease and drug associations

  • Versions: 5
  • Dependent Packages: 1
  • Dependent Repositories: 0
  • Downloads: 28,615 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Stargazers count: 8.1%
Average: 12.9%
Forks count: 14.4%
Downloads: 42.1%
Maintainers (1)
Spencer.Mahaffey@cuanschutz.edu
Last synced: 6 months ago