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multicrispr

https://github.com/loosolab/multicrispr

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 3 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    5 of 8 committers (62.5%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (4.2%) to scientific vocabulary

Keywords from Contributors

bioconductor-package gene genomics sequencing single-cell-rna-seq rna-seq proteomics human-cell-atlas single-cell ontology
Last synced: 9 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: loosolab
  • Language: HTML
  • Default Branch: master
  • Size: 5.15 MB
Statistics
  • Stars: 0
  • Watchers: 4
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 6 years ago · Last pushed over 4 years ago
Metadata Files
Readme

README.md

multicrispr: gRNA design

Installation

# Install multicrispr
    remotes::install_git('https://gitlab.gwdg.de/loosolab/software/multicrispr.git', 
                    repos = BiocManager::repositories())
# Install azimuth
    install.packages('reticulate')
    reticulate::conda_create('azienv', c('python=2.7'))
    reticulate::use_condaenv('azienv', required=TRUE)
    reticulate::py_install(c('azimuth', 'scikit-learn==0.17.1', 'biopython==1.76'), 'azienv', pip = TRUE)
# Index mm10 and hg38
    BiocManager::install('BSgenome.Mmusculus.UCSC.mm10')
    BiocManager::install('BSgenome.Hsapiens.UCSC.hg38')
    multicrispr::index_genome(BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10)
    multicrispr::index_genome(BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38)

Overview

Owner

  • Name: Looso bioinformatics lab
  • Login: loosolab
  • Kind: organization
  • Location: Bad Nauheim, Germany

Group of bioinformatics at the Max Planck Institute for Heart and Lung Research

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 408
  • Total Committers: 8
  • Avg Commits per committer: 51.0
  • Development Distribution Score (DDS): 0.064
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Aditya a****t@m****e 382
Aditya Bhagwat B****a@i****m 11
Nitesh Turaga n****a@g****m 6
jens.preussner j****r@m****e 4
rene.wiegandt r****t@m****e 2
Hervé Pagès h****s@f****g 1
johannes.graumann j****n@m****e 1
abhagwa_local a****l@K****e 1
Committer Domains (Top 20 + Academic)
mpi-bn.mpg.de: 4 ki-p0858.kerckhoff.mpg.de: 1 fredhutch.org: 1 indivumed.com: 1

Issues and Pull Requests

Last synced: over 1 year ago

All Time
  • Total issues: 1
  • Total pull requests: 1
  • Average time to close issues: 21 days
  • Average time to close pull requests: 32 minutes
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 7.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 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
  • templardrake (1)
Pull Request Authors
  • rwiegan (1)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

DESCRIPTION cran
  • R >= 4.0 depends
  • BSgenome * imports
  • BiocGenerics * imports
  • Biostrings * imports
  • CRISPRseek * imports
  • GenomeInfoDb * imports
  • GenomicFeatures * imports
  • GenomicRanges * imports
  • Rbowtie * imports
  • assertive * imports
  • data.table * imports
  • ggplot2 * imports
  • grid * imports
  • karyoploteR * imports
  • magrittr * imports
  • methods * imports
  • parallel * imports
  • plyranges * imports
  • reticulate * imports
  • rtracklayer * imports
  • stats * imports
  • stringi * imports
  • tidyr * imports
  • tidyselect * imports
  • utils * imports
  • AnnotationHub * suggests
  • BSgenome.Hsapiens.UCSC.hg38 * suggests
  • BSgenome.Mmusculus.UCSC.mm10 * suggests
  • BSgenome.Scerevisiae.UCSC.sacCer1 * suggests
  • BiocStyle * suggests
  • IRanges * suggests
  • TxDb.Mmusculus.UCSC.mm10.knownGene * suggests
  • ensembldb * suggests
  • knitr * suggests
  • magick * suggests
  • rmarkdown * suggests
  • testthat * suggests