hiReadsProcessor
This package is for version 3.19 of Bioconductor; for the stable, up-to-date release version, see hiReadsProcessor.
Functions to process LM-PCR reads from 454/Illumina data
Bioconductor version: 3.19
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("hiReadsProcessor")):
Installation
To install this package, start R (version "4.4") 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 | ||
| NEWS | Text |
Details
| biocViews | Preprocessing, Sequencing, Software |
| Version | 1.40.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (10 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
| 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 | hiReadsProcessor_1.40.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | hiReadsProcessor_1.40.0.tgz |
| macOS Binary (arm64) | hiReadsProcessor_1.40.0.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 |