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ORFik

https://github.com/roleren/orfik

Science Score: 49.0%

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
    Found .zenodo.json file
  • ✓
    DOI references
    Found 1 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    3 of 14 committers (21.4%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.4%) to scientific vocabulary

Keywords from Contributors

bioconductor-package gene genomics proteomics bioconductor bioinformatics immune-repertoire core-package u24ca289073 metagenomics
Last synced: 7 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: Roleren
  • License: mit
  • Language: R
  • Default Branch: master
  • Size: 5.16 MB
Statistics
  • Stars: 34
  • Watchers: 3
  • Forks: 9
  • Open Issues: 6
  • Releases: 0
Created over 10 years ago · Last pushed 7 months ago
Metadata Files
Readme Changelog License

README.md

ORFik: R package for discovery of novel genes.

bioc bioc

This package is published, but still under heavy development to include more features.

About

ORFik is a R package containing various functions for analysis of Ribo-Seq, RNA-Seq, CAGE and TCP-seq data related to transcriptomics. ORFik currently supports:

  1. Finding Open Reading Frames (very fast) in the genome of interest or on the set of transcripts/sequences.
  2. Hundreds of functions helping your analysis of either: sequence data, RNA-seq data, CAGE data, Ribo-seq data, TCP-seq data or RCP-seq data.
  3. Automatic estimations of RiboSeq footprint shift.
  4. Utilities for metaplots of RiboSeq coverage over gene START and STOP codons allowing to spot the shift.
  5. Shifting functions for the RiboSeq data.
  6. Annotation / re-annotation of 5' UTR Transcription Start Sites using CAGE data.
  7. Various measurements of gene identity, more than 30 functions. e.g. FLOSS, coverage, ORFscore, entropy that are recreated based on scientific publications.
  8. Utility functions to extend GenomicRanges for faster grouping, splitting, filtering etc. Included c++ function for speed.
  9. Extensive implemented syntax for coverage and metacoverage of NGS data, including smart grouping functions for easier prototyping.
  10. Automatic download of genome annotation from any species supported by ensembl.
  11. Automatic download and metadata extraction of NGS files from SRA, ERA, DRA and GEO.
  12. Full NGS alignment pipeline: Trimming data using fastp and alignment using STAR (with optional contaminant removals)
  13. Simplifying working with massive amounts of datasets using the ORFik experiment class.

Installation

Package is available from bioconductor (Stable branch, R version >= 4.0.0) r if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("ORFik")

Development version on bioconductor (Devel branch, R version >= 4.0.0) r if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("ORFik", version = "devel")

Package is also available here on github (Experimental branch, R version >= 4.1.0) r if (!requireNamespace("remotes", quietly=TRUE)) install.packages("remotes") remotes::install_github("Roleren/ORFik")

More information

After installation run: ```r library(ORFik)

NGS metadata extraction

?download.SRA.metadata

NGS data download

?download.SRA

Annotation download

?getGenomeAndAnnotation

Data management

?create.experiment

NGS Library Quality control

?ORFikQC

Tissue specific 5' utrs using cage-data

?reassignTSSbyCage

Detecting open reading frames

?findORFs

get a feature-set from predicted orfs

?computeFeatures

read vignette (tutorials)

browseVignettes("ORFik") ```
Please read Bioconductor vignettes for detailed tutorials and examples.

Feedback

Please feel free to provide feedback or desired functionality by creating a new issue on our github page.

Owner

  • Name: Håkon Tjeldnes
  • Login: Roleren
  • Kind: user
  • Location: Bergen, Norway

Currently doing a phd in bioinformatics at University of Bergen.

GitHub Events

Total
  • Issues event: 12
  • Watch event: 2
  • Issue comment event: 40
  • Push event: 75
  • Fork event: 1
Last Year
  • Issues event: 12
  • Watch event: 2
  • Issue comment event: 40
  • Push event: 75
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 941
  • Total Committers: 14
  • Avg Commits per committer: 67.214
  • Development Distribution Score (DDS): 0.071
Past Year
  • Commits: 136
  • Committers: 5
  • Avg Commits per committer: 27.2
  • Development Distribution Score (DDS): 0.081
Top Committers
Name Email Commits
Roleren h****n@h****m 874
JokingHero k****n@g****m 25
Nitesh Turaga n****a@g****m 14
Kornel Labun k****n@g****m 9
Michal Swirski m****i@s****l 5
vobencha v****a@g****m 2
J Wokaty j****y@s****u 2
vobencha v****n@r****g 2
J Wokaty j****y 2
Assa Yeroslaviz y****z@b****e 2
Krzysztof Starecki k****i@g****m 1
Kayla-Morrell k****l@r****g 1
Hervé Pagès h****b@g****m 1
LiNk-NY m****z@r****g 1
Committer Domains (Top 20 + Academic)
roswellpark.org: 3 biochem.mpg.de: 1 sph.cuny.edu: 1 student.uw.edu.pl: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 6
  • Total pull requests: 0
  • Average time to close issues: 4 months
  • Average time to close pull requests: N/A
  • Total issue authors: 5
  • Total pull request authors: 0
  • Average comments per issue: 7.17
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 4
  • Pull requests: 0
  • Average time to close issues: about 1 month
  • Average time to close pull requests: N/A
  • Issue authors: 4
  • Pull request authors: 0
  • Average comments per issue: 8.75
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • SuhasSrinivasan (17)
  • Arek86 (3)
  • josiegleeson (2)
  • johannesnicolaus (1)
  • 1127yangyuping (1)
  • NastiaSkuba (1)
  • m-jahn (1)
  • JC-therea (1)
  • lundlab (1)
  • hpages (1)
  • matanel-y (1)
  • josefinaperalba (1)
  • csittz (1)
Pull Request Authors
  • SuhasSrinivasan (1)
  • upgradedavid (1)
  • hpages (1)
Top Labels
Issue Labels
bug (1) enhancement (1)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 23,933 total
  • Total dependent packages: 2
  • Total dependent repositories: 0
  • Total versions: 10
  • Total maintainers: 1
bioconductor.org: ORFik

Open Reading Frames in Genomics

  • Versions: 10
  • Dependent Packages: 2
  • Dependent Repositories: 0
  • Downloads: 23,933 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 15.6%
Downloads: 46.7%
Maintainers (1)
hauken_heyken@hotmail.com
Last synced: 7 months ago

Dependencies

DESCRIPTION cran
  • GenomicAlignments >= 1.19.0 depends
  • GenomicRanges >= 1.35.1 depends
  • IRanges >= 2.17.1 depends
  • R >= 3.6.0 depends
  • AnnotationDbi >= 1.45.0 imports
  • BSgenome * imports
  • BiocGenerics >= 0.29.1 imports
  • BiocParallel >= 1.19.0 imports
  • Biostrings >= 2.51.1 imports
  • DESeq2 >= 1.24.0 imports
  • GGally >= 1.4.0 imports
  • GenomeInfoDb >= 1.15.5 imports
  • GenomicFeatures >= 1.31.10 imports
  • R.utils * imports
  • Rcpp >= 1.0.0 imports
  • Rsamtools >= 1.35.0 imports
  • S4Vectors >= 0.21.3 imports
  • SummarizedExperiment >= 1.14.0 imports
  • biomartr * imports
  • cowplot >= 1.0.0 imports
  • data.table >= 1.11.8 imports
  • fst >= 0.9.2 imports
  • ggplot2 >= 2.2.1 imports
  • gridExtra >= 2.3 imports
  • httr >= 1.3.0 imports
  • jsonlite * imports
  • methods >= 3.6.0 imports
  • rtracklayer >= 1.43.0 imports
  • stats * imports
  • tools * imports
  • utils * imports
  • xml2 >= 1.2.0 imports
  • BSgenome.Hsapiens.UCSC.hg19 * suggests
  • BiocStyle * suggests
  • knitr * suggests
  • rmarkdown * suggests
  • testthat * suggests