DuplexDiscovereR
This is the development version of DuplexDiscovereR; for the stable release version, see DuplexDiscovereR.
Analysis of the data from RNA duplex probing experiments
Bioconductor version: Development (3.21)
DuplexDiscovereR is a package designed for analyzing data from RNA cross-linking and proximity ligation protocols such as SPLASH, PARIS, LIGR-seq, and others. DuplexDiscovereR accepts input in the form of chimerically or split-aligned reads. It includes procedures for alignment classification, filtering, and efficient clustering of individual chimeric reads into duplex groups (DGs). Once DGs are identified, the package predicts RNA duplex formation and their hybridization energies. Additional metrics, such as p-values for random ligation hypothesis or mean DG alignment scores, can be calculated to rank final set of RNA duplexes. Data from multiple experiments or replicates can be processed separately and further compared to check the reproducibility of the experimental method.
Author: Egor Semenchenko [aut, cre, cph] (ORCID:
Maintainer: Egor Semenchenko <yegor.smb at gmail.com>
citation("DuplexDiscovereR")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("DuplexDiscovereR")
For older versions of R, please refer to the appropriate Bioconductor release.
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("DuplexDiscovereR")| DuplexDiscovereR tutorial | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Clustering, Sequencing, Software, SplicedAlignment, StructuralPrediction, Transcriptomics |
| Version | 1.1.0 |
| In Bioconductor since | BioC 3.20 (R-4.4) (< 6 months) |
| License | GPL-3 |
| Depends | R (>= 4.4), InteractionSet |
| Imports | Gviz, Biostrings, rtracklayer, GenomicAlignments, GenomicRanges, ggsci, igraph, rlang, scales, stringr, dplyr, tibble, tidyr, purrr, methods, grDevices, stats, utils |
| System Requirements | |
| URL | https://github.com/Egors01/DuplexDiscovereR/ |
| Bug Reports | https://github.com/Egors01/DuplexDiscovereR/issues/ |
See More
| Suggests | knitr, UpSetR, BiocStyle, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | DuplexDiscovereR_1.1.0.tar.gz |
| Windows Binary (x86_64) | DuplexDiscovereR_1.1.0.zip |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/DuplexDiscovereR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/DuplexDiscovereR |
| Bioc Package Browser | https://code.bioconductor.org/browse/DuplexDiscovereR/ |
| Package Short Url | https://bioconductor.org/packages/DuplexDiscovereR/ |
| Package Downloads Report | Download Stats |