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factr

factR: Functional Annotation of Custom-assembled Transcripts in R

https://github.com/fursham-h/factr

Science Score: 10.0%

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Keywords

custom-transcriptomes functional-annotation gtf rna-seq-analysis

Keywords from Contributors

bioconductor-package gene grna-sequence immune-repertoire ontology
Last synced: 6 months ago · JSON representation

Repository

factR: Functional Annotation of Custom-assembled Transcripts in R

Basic Info
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 0
  • Open Issues: 1
  • Releases: 0
Topics
custom-transcriptomes functional-annotation gtf rna-seq-analysis
Created about 6 years ago · Last pushed over 2 years ago
Metadata Files
Readme License

README.md

factR v.1

Functional Annotation of Custom Transcriptomes in R

R build status Codecov test coverage Codecov test coverage <!-- badges: end -->

General workflow

factR is a robust and easy-to-use R package with tools to process custom-assembled transcriptomes (GTF). Below are factR's key functions:

  • Core features
    1. Construct transcript coding (CDS) information using a reference-guided process
    2. Predict protein domains on coding transcripts
    3. Predict sensitivity of coding transcripts to Nonsense-mediated decay
  • Supporting features
    1. Match chromosome levels of query GTF/object to reference annotation
    2. Match geneid and genenames of query GTF to reference annotation
    3. Plot transcripts from GTF GRanges object using wiggleplotr
    4. Subset new transcripts from custom transcriptome

How to install

The latest stable version can be installed directly from Bioconductor: r if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("factR")

Alternatively, you may install the development version of factR using devtools: ```r

install.packages("devtools")

devtools::install_github("fursham-h/factR") ```

Getting started

See our quickstart guide or our full vignette on how to get started

Acknowledgements

We thank Kaur Alasoo for sharing code resources for wiggleplotr and for valuable discussions on the design of the package.

Citing factR

Please cite the following references if you use factR:

  1. Fursham Hamid, Kaur Alasoo, Jaak Vilo, Eugene Makeyev (2022); Functional annotation of custom transcriptomes; Methods in Molecular Biology
  2. Fursham Hamid (2022); Functional Annotation of Custom Transcriptomes; Bioconductor

Owner

  • Name: Fursham Hamid
  • Login: fursham-h
  • Kind: user
  • Location: London
  • Company: King's College London

Lecturer in Bioinformatics at the Centre for Developmental Neurobiology

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 512
  • Total Committers: 5
  • Avg Commits per committer: 102.4
  • Development Distribution Score (DDS): 0.602
Past Year
  • Commits: 16
  • Committers: 3
  • Avg Commits per committer: 5.333
  • Development Distribution Score (DDS): 0.25
Top Committers
Name Email Commits
Fursham 3****m 204
Fursham Hamid f****h@g****m 157
“Fursham” “****h@g****” 147
J Wokaty j****y 2
J Wokaty j****y@s****u 2
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 1 gmail.com”: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 2
  • Total pull requests: 4
  • Average time to close issues: 2 months
  • Average time to close pull requests: 2 minutes
  • Total issue authors: 2
  • Total pull request authors: 1
  • Average comments per issue: 1.5
  • Average comments per pull request: 0.0
  • Merged pull requests: 4
  • 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
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Top Authors
Issue Authors
  • jcotney (1)
  • Drosofriends (1)
Pull Request Authors
  • fursham-h (4)
Top Labels
Issue Labels
enhancement (1)
Pull Request Labels

Dependencies

DESCRIPTION cran
  • R >= 4.2 depends
  • BiocGenerics >= 0.38 imports
  • BiocParallel imports
  • Biostrings >= 2.60 imports
  • GenomeInfoDb >= 1.28 imports
  • GenomicFeatures >= 1.44 imports
  • GenomicRanges >= 1.44 imports
  • IRanges >= 2.26 imports
  • RCurl >= 1.98 imports
  • S4Vectors >= 0.30 imports
  • XML >= 3.99 imports
  • crayon * imports
  • data.table >= 1.14 imports
  • dplyr >= 1.0 imports
  • drawProteins >= 1.12 imports
  • ggplot2 >= 3.3 imports
  • graphics >= 4.1 imports
  • methods >= 4.0 imports
  • pbapply >= 1.5 imports
  • purrr >= 0.3 imports
  • rlang >= 1.0 imports
  • rtracklayer >= 1.52 imports
  • stats >= 4.1 imports
  • stringr >= 1.4 imports
  • tibble >= 3.1 imports
  • tidyr >= 1.1 imports
  • utils >= 4.1 imports
  • wiggleplotr >= 1.16 imports
  • AnnotationHub >= 2.22 suggests
  • BSgenome >= 1.58 suggests
  • BSgenome.Mmusculus.UCSC.mm10 * suggests
  • bio3d >= 2.4 suggests
  • covr * suggests
  • knitr * suggests
  • markdown * suggests
  • patchwork * suggests
  • rmarkdown * suggests
  • rmdformats * suggests
  • signalHsmm >= 1.5 suggests
  • testthat * suggests
  • tidyverse >= 1.3 suggests
  • zeallot * suggests
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.github/workflows/test-coverage.yaml actions
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