posDemux
This is the released version of posDemux; for the devel version, see posDemux.
Positional combinatorial sequence demultiplexer
Bioconductor version: Release (3.23)
Demultiplexing and filtering utilities intended for reads with combinatorial barcodes (i.e. PETRI-seq and SPLiT-seq). The demultiplexer algorithm uses the position of the segments to extract and compare the barcodes with the reference (whitelist). A Shiny application is provided to interactively select cutoffs for which barcode combinations to keep.
Author: Jakob Peder Pettersen [aut, cre]
, Centre for new antibacterial strategies (CANS) [fnd]
Maintainer: Jakob Peder Pettersen <jakobpeder.pettersen at gmail.com>
citation("posDemux")):
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")
BiocManager::install("posDemux")
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("posDemux")| Demultiplexing with streaming | HTML | R Script |
| Introduction to combinatorial demultiplexing | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | RNASeq, SequenceMatching, Sequencing, Software |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.23 (R-4.6) (< 6 months) |
| License | AGPL (>= 3) |
| Depends | R (>= 4.6.0) |
| Imports | Biostrings, ggplot2, methods, assertthat, glue, magrittr, dplyr, rlang, ShortRead, readr, shiny, purrr |
| System Requirements | |
| URL | https://github.com/yaccos/posDemux https://yaccos.github.io/posDemux/ |
| Bug Reports | https://github.com/yaccos/posDemux/issues |
See More
| Suggests | testthat, devtools, DNABarcodes, knitr, rmarkdown, tibble, tidyr, BiocStyle, RefManageR, sessioninfo, DBI, chunked, RSQLite, dbplyr |
| Linking To | Rcpp, Biostrings, IRanges, S4Vectors, XVector |
| 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 | posDemux_1.0.0.tar.gz |
| Windows Binary (x86_64) | posDemux_1.0.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | posDemux_1.0.0.tgz |
| macOS Binary (sonoma-arm64) | posDemux_1.0.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/posDemux |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/posDemux |
| Bioc Package Browser | https://code.bioconductor.org/browse/posDemux/ |
| Package Short Url | https://bioconductor.org/packages/posDemux/ |
| Package Downloads Report | Download Stats |