WithinHostExperiment
This is the development version of WithinHostExperiment; to use it, please install the devel version of Bioconductor.
Within-Host Pathogen Variant QC, Diversity, and Bottleneck
Bioconductor version: Development (3.24)
Provides a SummarizedExperiment-based container and workflow functions for analysing intra-host single nucleotide variants (iSNV) from pathogen deep sequencing data. Supports replicate-aware quality control with full provenance tracking, multi-caller import harmonisation, within-host diversity quantification, and standardised export to transmission bottleneck estimation tools. Designed as infrastructure that bridges upstream variant callers (iVar, LoFreq, Freebayes) with downstream analysis packages through a common data object with uncertainty-preserving QC.
Author: Cuiwei Gao [aut, cre]
Maintainer: Cuiwei Gao <48gaocuiwei at gmail.com>
citation("WithinHostExperiment")):Cuiwei Gao. WithinHostExperiment: Within-Host Pathogen Variant QC, Diversity, and Bottleneck. doi:10.18129/B9.bioc.WithinHostExperiment, R package version 0.99.2, https://bioconductor.org/packages/WithinHostExperiment.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("WithinHostExperiment")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("WithinHostExperiment")| Introduction to WithinHostExperiment | HTML | R Script |
| Reference Manual |
Details
| biocViews | DataImport, Genetics, GenomicVariation, QualityControl, Sequencing, Software, VariantAnnotation, VariantDetection |
| Version | 0.99.2 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0) |
| Imports | methods, BiocGenerics, S4Vectors (>= 0.32.0), IRanges, GenomicRanges, SummarizedExperiment, GenomeInfoDb, Biostrings, GenomicFeatures, VariantAnnotation, graphics, stats, tools, utils |
| System Requirements | |
| URL | https://github.com/CuiweiG/WithinHostExperiment |
| Bug Reports | https://github.com/CuiweiG/WithinHostExperiment/issues |
See More
| Suggests | BiocStyle, ggplot2 (>= 3.4.0), patchwork, testthat (>= 3.1.5), knitr, rmarkdown, BiocCheck, rtracklayer, txdbmaker, MSA2dist |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | WithinHostExperiment_0.99.2.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/WithinHostExperiment |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/WithinHostExperiment |
| Package Short Url | https://bioconductor.org/packages/WithinHostExperiment/ |
| Package Downloads Report | Download Stats |