PICB
This is the development version of PICB; to use it, please install the devel version of Bioconductor.
piRNA Cluster Builder
Bioconductor version: Development (3.21)
piRNAs (short for PIWI-interacting RNAs) and their PIWI protein partners play a key role in fertility and maintaining genome integrity by restricting mobile genetic elements (transposons) in germ cells. piRNAs originate from genomic regions known as piRNA clusters. The piRNA Cluster Builder (PICB) is a versatile toolkit designed to identify genomic regions with a high density of piRNAs. It constructs piRNA clusters through a stepwise integration of unique and multimapping piRNAs and offers wide-ranging parameter settings, supported by an optimization function that allows users to test different parameter combinations to tailor the analysis to their specific piRNA system. The output includes extensive metadata columns, enabling researchers to rank clusters and extract cluster characteristics.
Author: Pavol Genzor [aut], Aleksandr Friman [aut], Daniel Stoyko [aut], Parthena Konstantinidou [aut], Franziska Ahrend [aut, cre] (ORCID:
Maintainer: Franziska Ahrend <haase-lab-bioinfo at nih.gov>
citation("PICB")):
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("PICB")
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("PICB")| Introduction to the piRNA Cluster Builder (PICB) | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Coverage, FunctionalPrediction, Genetics, GenomeAnnotation, Sequencing, Software, Transcriptomics |
| Version | 0.99.15 |
| In Bioconductor since | BioC 3.21 (R-4.5) |
| License | CC0 |
| Depends | |
| Imports | utils, GenomicRanges, GenomicAlignments, GenomeInfoDb, Biostrings, Rsamtools, data.table, IRanges, seqinr, stats, openxlsx, dplyr, S4Vectors, methods |
| System Requirements | |
| URL | https://github.com/HaaseLab/PICB |
| Bug Reports | https://github.com/HaaseLab/PICB/issues |
See More
| Suggests | knitr, rtracklayer, testthat, BiocStyle, prettydoc, BSgenome, BSgenome.Dmelanogaster.UCSC.dm6, BiocManager, rmarkdown, ggplot2 |
| 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 | PICB_0.99.15.tar.gz |
| Windows Binary (x86_64) | PICB_0.99.15.zip |
| macOS Binary (x86_64) | PICB_0.99.15.tgz |
| macOS Binary (arm64) | PICB_0.99.15.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/PICB |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/PICB |
| Bioc Package Browser | https://code.bioconductor.org/browse/PICB/ |
| Package Short Url | https://bioconductor.org/packages/PICB/ |
| Package Downloads Report | Download Stats |