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hiReadsProcessor

This is the development version of hiReadsProcessor; for the stable release version, see hiReadsProcessor.

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

Bioconductor version: Development (3.18)

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 (version "4.3") and enter: 

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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")
Using hiReadsProcessor HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews Preprocessing, Sequencing, Software
Version 1.37.0
In Bioconductor since BioC 3.0 (R-3.1) (9 years)
License GPL-3
Depends R (>= 3.5.0), Biostrings, GenomicAlignments, BiocParallel, hiAnnotator
Imports sonicLength, dplyr, BiocGenerics, GenomicRanges, readxl, methods
Linking To
Suggests knitr, testthat, markdown
System Requirements BLAT, UCSC hg18 in 2bit format for BLAT
Enhances
URL
See More
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

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

Source Package hiReadsProcessor_1.37.0.tar.gz
Windows Binary
macOS Binary (x86_64) hiReadsProcessor_1.37.0.tgz
macOS Binary (arm64) hiReadsProcessor_1.37.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/hiReadsProcessor
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/hiReadsProcessor
Bioc Package Browser https://code.bioconductor.org/browse/hiReadsProcessor/
Package Short Url https://bioconductor.org/packages/hiReadsProcessor/
Package Downloads Report Download Stats