hiReadsProcessor

This package is for version 3.21 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see hiReadsProcessor.

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

DOI: 10.18129/B9.bioc.hiReadsProcessor

Bioconductor version: 3.21

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 "4.5") and enter:


if (!require("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")

Using hiReadsProcessor HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews Preprocessing, Sequencing, Software

Version 1.44.0

In Bioconductor since BioC 3.0 (R-3.1) (11 years)

License GPL-3

Depends R (>= 3.5.0), Biostrings, pwalign, GenomicAlignments, BiocParallel, hiAnnotator

Imports sonicLength, dplyr, BiocGenerics, GenomicRanges, readxl, methods

System Requirements BLAT, UCSC hg18 in 2bit format for BLAT

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Suggests knitr, testthat, markdown

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Package Archives

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

Source Package hiReadsProcessor_1.44.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64) hiReadsProcessor_1.44.0.tgz

macOS Binary (arm64) hiReadsProcessor_1.44.0.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/

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