To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("hiReadsProcessor")

In most cases, you don't need to download the package archive at all.

hiReadsProcessor

This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see hiReadsProcessor.

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

Bioconductor version: 3.2

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>

Citation (from within R, enter citation("hiReadsProcessor")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("hiReadsProcessor")

Documentation

To view documentation for the version of this package installed in your system, start R and enter: 

browseVignettes("hiReadsProcessor")
HTML Introduction
PDF Reference Manual
Text NEWS

Details

biocViews Preprocessing, Sequencing, Software
Version 1.6.0
In Bioconductor since BioC 3.0 (R-3.1) (1.5 years)
License GPL-3
Depends Biostrings, GenomicAlignments, xlsx, BiocParallel, hiAnnotator, R (>= 3.0)
Imports sonicLength, dplyr, GenomicRanges, BiocGenerics, rSFFreader
LinkingTo
Suggests knitr, testthat
SystemRequirements BLAT, UCSC hg18 in 2bit format for BLAT
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Build Report

Package Archives

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

Package Source hiReadsProcessor_1.6.0.tar.gz
Windows Binary hiReadsProcessor_1.6.0.zip
Mac OS X 10.6 (Snow Leopard) hiReadsProcessor_1.6.0.tgz
Mac OS X 10.9 (Mavericks) hiReadsProcessor_1.6.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/hiReadsProcessor/tree/release-3.2
Package Short Url http://bioconductor.org/packages/hiReadsProcessor/
Package Downloads Report Download Stats

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