pram
An R/Bioconductor package to predict intergenic transcript models from RNA-seq
Science Score: 23.0%
This score indicates how likely this project is to be science-related based on various indicators:
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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 2 DOI reference(s) in README -
○Academic publication links
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✓Committers with academic emails
1 of 3 committers (33.3%) from academic institutions -
○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (13.0%) to scientific vocabulary
Keywords
Repository
An R/Bioconductor package to predict intergenic transcript models from RNA-seq
Basic Info
- Host: GitHub
- Owner: pliu55
- Language: R
- Default Branch: master
- Homepage: https://bioconductor.org/packages/pram
- Size: 3.8 MB
Statistics
- Stars: 1
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
PRAM: Pooling RNA-seq and Assembling Models
Table of Contents
Introduction
Pooling RNA-seq and Assembling Models (PRAM) is an Bioconductor R package that utilizes multiple RNA-seq datasets to predict transcript models. The workflow of PRAM contains four steps, which is shown in the figure below with function names and associated key parameters. PRAM has a vignette that describes each function in details.
Installation
From GitHub
Start R and enter:
r
devtools::install_github('pliu55/pram')
From Bioconductor
Start R and enter:
r
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("pram")
Reference
PRAM: a novel pooling approach for discovering intergenic transcripts from large-scale RNA sequencing experiments. Peng Liu, Alexandra A. Soukup, Emery H. Bresnick, Colin N. Dewey, and Sündüz Keleş. Genome Research 2020. 30:1655-1666
For key results reported in the PRAM manuscript and scripts for reproducibility, please check out this GitHub repository.
Contact
Got a question? Please report it at the issues tab in this repository.
License
PRAM is licensed under the GNU General Public License v3.
Owner
- Name: Peng Liu
- Login: pliu55
- Kind: user
- Company: UW-Madison
- Website: https://www.ncbi.nlm.nih.gov/myncbi/peng.liu.7/bibliography/public/
- Repositories: 3
- Profile: https://github.com/pliu55
GitHub Events
Total
Last Year
Committers
Last synced: over 2 years ago
Top Committers
| Name | Commits | |
|---|---|---|
| Peng Liu | p****5@w****u | 443 |
| Peng Liu | p****5 | 9 |
| Nitesh Turaga | n****a@g****m | 2 |
Committer Domains (Top 20 + Academic)
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 0
- Total pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Total issue authors: 0
- Total 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
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
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Pull Request Authors
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 9,796 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 5
- Total maintainers: 1
bioconductor.org: pram
Pooling RNA-seq datasets for assembling transcript models
- Homepage: https://github.com/pliu55/pram
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/pram/inst/doc/pram.pdf
- License: GPL (>= 3)
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Latest release: 1.24.0
published about 1 year ago
Rankings
Maintainers (1)
Dependencies
- R >= 3.6 depends
- BiocGenerics imports
- BiocParallel * imports
- GenomeInfoDb imports
- GenomicAlignments >= 1.16.0 imports
- GenomicRanges imports
- IRanges imports
- Rsamtools imports
- S4Vectors imports
- data.table imports
- methods * imports
- rtracklayer imports
- tools * imports
- utils * imports
- BiocStyle * suggests
- knitr * suggests
- rmarkdown * suggests
- testthat * suggests