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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 (>= 4.6.0) |
| 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 |
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 |
| Bioc Package Browser | https://code.bioconductor.org/browse/WithinHostExperiment/ |
| Package Short Url | https://bioconductor.org/packages/WithinHostExperiment/ |
| Package Downloads Report | Download Stats |