Science Score: 23.0%
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○CITATION.cff file
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○codemeta.json file
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○.zenodo.json file
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✓DOI references
Found 4 DOI reference(s) in README -
○Academic publication links
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3 of 6 committers (50.0%) from academic institutions -
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Low similarity (13.8%) to scientific vocabulary
Keywords from Contributors
Repository
periodicDNA R package
Basic Info
- Host: GitHub
- Owner: js2264
- License: gpl-3.0
- Language: R
- Default Branch: master
- Homepage: https://js2264.github.io/periodicDNA
- Size: 75 MB
Statistics
- Stars: 6
- Watchers: 0
- Forks: 3
- Open Issues: 0
- Releases: 0
Metadata Files
README.md
periodicDNA 
Introduction
This R package helps the user identify k-mers (e.g. di- or tri-nucleotides) present periodically in a set of genomic loci (typically regulatory elements). It is not aimed at identifying motifs separated by a conserved distance; for this type of analysis, please visit MEME website.
Installation
periodicDNA is available in Bioconductor. To install the current release use:
r
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("periodicDNA")
For advanced users, the most recent periodicDNA can be installed from Github as follows (might be buggy):
r
install.packages("devtools")
devtools::install_github("js2264/periodicDNA")
library(periodicDNA)
Citation
If you are using periodicDNA in your research, please cite:
periodicDNA: an R/Bioconductor package to investigate k-mer periodicity in DNA
J. Serizay & J. Ahringer
F1000Research, 2021Distinctive regulatory architectures of germline-active and somatic genes in C. elegans
J. Serizay, Y. Dong, J. Jänes, M. Chesney, C. Cerrato & J. Ahringer
Genome Research, 2020
How to use periodicDNA
periodicDNA includes a vignette where its usage is illustrated. To access the vignette, please use:
r
vignette('periodicDNA')
Main functions
The two main user-level functions of periodicDNA are getPeriodicity() and
getPeriodicityTrack().
getPeriodicity()is used to compute the power spectral density (PSD) of a chosen k-mer (i.e.TT) in a set of sequences. The PSD score at a given period indicates the strength of the k-mer at this period.getPeriodicityTrack()can be used to generate linear tracks representing the periodicity strength of a given k-mer at a chosen period, over genomic loci of interest.
getPeriodicity() function
r
data(ce11_TSSs)
PSDs <- getPeriodicity(
ce11_TSSs[['Ubiq.']],
genome = 'BSgenome.Celegans.UCSC.ce11',
motif = 'TT',
BPPARAM = MulticoreParam(12),
n_shuffling = 100
)
plotPeriodicityResults(PSDs)
getPeriodicityTrack() function
r
data(ce11_proms)
WW_10bp <- getPeriodicityTrack(
genome = 'BSgenome.Celegans.UCSC.ce11',
granges = ce11_proms,
motif = 'WW',
period = 10,
bw_file = 'WW-10-bp-periodicity_over-proms.bw',
BPPARAM = MulticoreParam(12)
)
Warning: It is recommended to run this command across many processors
using BiocParallel. This command typically takes one day to produce
a periodicity track over 15,000 GRanges of 150 bp (with default parameters)
using BPPARAM = MulticoreParam(12).
It is highly recommended to run this command in a new screen session.
Contributions
Code contributions, bug reports, fixes and feature requests are most welcome. Please make any pull requests against the master branch at https://github.com/js2264/periodicityDNA and file issues at https://github.com/js2264/periodicityDNA/issues
License
periodicDNA is licensed under the GPL-3 license.
Owner
- Name: Jacques Serizay
- Login: js2264
- Kind: user
- Location: Paris, FR
- Website: js2264.github.io
- Repositories: 12
- Profile: https://github.com/js2264
GitHub Events
Total
Last Year
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| js2264 | j****4@c****k | 137 |
| Jacques Serizay | j****4@c****k | 13 |
| Nitesh Turaga | n****a@g****m | 8 |
| js2264 | j****y@g****m | 7 |
| J Wokaty | j****y@s****u | 2 |
| Hervé Pagès | h****b@g****m | 1 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 0
- Total pull requests: 1
- Average time to close issues: N/A
- Average time to close pull requests: about 1 month
- Total issue authors: 0
- Total pull request authors: 1
- Average comments per issue: 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
Top Authors
Issue Authors
Pull Request Authors
- codacy-badger (1)
Top Labels
Issue Labels
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Packages
- Total packages: 1
-
Total downloads:
- bioconductor 7,895 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: periodicDNA
Set of tools to identify periodic occurrences of k-mers in DNA sequences
- Homepage: https://github.com/js2264/periodicDNA
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/periodicDNA/inst/doc/periodicDNA.pdf
- License: GPL-3 + file LICENSE
-
Latest release: 1.18.0
published about 1 year ago