To install this package, start R and enter:

source("http://bioconductor.org/biocLite.R")
biocLite("hiReadsProcessor")

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

hiReadsProcessor

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

Bioconductor version: 3.0

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:

source("http://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 R Script Introduction
PDF   Reference Manual
Text   NEWS

Details

biocViews Preprocessing, Sequencing, Software
Version 1.0.0
In Bioconductor since BioC 3.0 (R-3.1)
License GPL-3
Depends Biostrings, GenomicAlignments, xlsx, BiocParallel, hiAnnotator, R (>= 3.0)
Imports sonicLength, plyr
LinkingTo
Suggests knitr, testthat, BiocGenerics, rSFFreader
SystemRequirements BLAT, JRE, 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_1.0.0.tar.gz
Windows Binary hiReadsProcessor_1.0.0.zip
Mac OS X 10.6 (Snow Leopard) hiReadsProcessor_1.0.0.tgz
Mac OS X 10.9 (Mavericks) hiReadsProcessor_1.0.0.tgz
Browse/checkout source (username/password: readonly)
Package Downloads Report Download Stats

Mailing Lists »

Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!

Fred Hutchinson Cancer Research Center