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Bioconductor - hiReadsProcessor (development version)

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 (3.22)

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")

# 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")
Details biocViews Preprocessing, Sequencing, Software Version 1.45.0 In Bioconductor since BioC 3.0 (R-3.1) (10.5 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 URL See More Package Archives

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

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