Registration and Call for Abstracts Open for Bioc2024

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 (3.19)

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 "4.4") 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

Reference Manual PDF

Details

biocViews Preprocessing, Sequencing, Software
Version 1.39.0
In Bioconductor since BioC 3.0 (R-3.1) (9.5 years)
License GPL-3
Depends Biostrings, GenomicAlignments, BiocParallel, hiAnnotator, R (>= 3.0)
Imports sonicLength, dplyr, BiocGenerics, GenomicRanges, readxl, methods
System Requirements BLAT, UCSC hg18 in 2bit format for BLAT
URL
See More
Suggests knitr, testthat, markdown
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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 https://bioconductor.org/packages/hiReadsProcessor/
Package Downloads Report Download Stats