DOI: 10.18129/B9.bioc.hiReadsProcessor  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see hiReadsProcessor.

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

Bioconductor version: 3.16

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")):


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biocViews Preprocessing, Sequencing, Software
Version 1.34.0
In Bioconductor since BioC 3.0 (R-3.1) (8.5 years)
License GPL-3
Depends R (>= 3.5.0), Biostrings, GenomicAlignments, BiocParallel, hiAnnotator
Imports sonicLength, dplyr, BiocGenerics, GenomicRanges, readxl, methods
Suggests knitr, testthat, markdown
SystemRequirements BLAT, UCSC hg18 in 2bit format for BLAT
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Source Package hiReadsProcessor_1.34.0.tar.gz
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macOS Binary (x86_64) hiReadsProcessor_1.34.0.tgz
macOS Binary (arm64) hiReadsProcessor_1.34.0.tgz
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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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