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hiReadsProcessor
This package isdeprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information.
This package is for version 3.22 of Bioconductor.This package has been removed from Bioconductor.For the last stable, up-to-date release version, seehiReadsProcessor.
Functions to process LM-PCR reads from 454/Illumina data
Bioconductor version: Release (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("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 appropriateBioconductor release.
Documentation
| Reference Manual |
Details
| biocViews | Preprocessing,Sequencing,Software |
| Version | 1.46.0 |
| In Bioconductor since | BioC 3.0 (R-3.1) (11 years) |
| License | GPL-3 |
| Depends | Biostrings,pwalign,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 |
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| Build Report | Build Report |
Package Archives
FollowInstallation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| 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 |