hiReadsProcessor

DOI: 10.18129/B9.bioc.hiReadsProcessor    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see hiReadsProcessor.

Functions to process LM-PCR reads from 454/Illumina data

Bioconductor version: 3.8

hiReadsProcessor contains set of functions which allow users to process LM-PCR products sequenced using any platform. Given an excel/txt file containing parameters for demultiplexing and sample metadata, the functions automate trimming of adaptors and identification of the genomic product. Genomic products are further processed for QC and abundance quantification.

Author: Nirav V Malani <malnirav at gmail.com>

Maintainer: Nirav V Malani <malnirav at gmail.com>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("hiReadsProcessor")

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("hiReadsProcessor")

 

HTML	R Script	Using hiReadsProcessor
PDF		Reference Manual
Text		NEWS

Details

biocViews	Preprocessing, Sequencing, Software
Version	1.18.0
In Bioconductor since	BioC 3.0 (R-3.1) (4.5 years)
License	GPL-3
Depends	Biostrings, GenomicAlignments, BiocParallel, hiAnnotator, R (>= 3.0)
Imports	sonicLength, dplyr, BiocGenerics, GenomicRanges, rSFFreader, readxl, methods
LinkingTo
Suggests	knitr, testthat
SystemRequirements	BLAT, UCSC hg18 in 2bit format for BLAT
Enhances
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	hiReadsProcessor_1.18.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)	hiReadsProcessor_1.18.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/hiReadsProcessor
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/hiReadsProcessor
Package Short Url	http://bioconductor.org/packages/hiReadsProcessor/
Package Downloads Report	Download Stats