DOI: 10.18129/B9.bioc.hiReadsProcessor    

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

Bioconductor version: Release (3.7)

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")):


To install this package, start R and enter:

## try http:// if https:// URLs are not supported


HTML R Script Using hiReadsProcessor
PDF   Reference Manual
Text   NEWS


biocViews Preprocessing, Sequencing, Software
Version 1.16.0
In Bioconductor since BioC 3.0 (R-3.1) (3.5 years)
License GPL-3
Depends Biostrings, GenomicAlignments, BiocParallel, hiAnnotator, R (>= 3.0)
Imports sonicLength, dplyr, BiocGenerics, GenomicRanges, rSFFreader, readxl, methods
Suggests knitr, testthat
SystemRequirements BLAT, UCSC hg18 in 2bit format for BLAT
Depends On Me
Imports Me
Suggests Me
Build Report  

Package Archives

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

Source Package hiReadsProcessor_1.16.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan) hiReadsProcessor_1.16.0.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

Documentation »


R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: