posDemux
This is the development version of posDemux; to use it, please install the devel version of Bioconductor.
Positional combinatorial sequence demultiplexer
Bioconductor version: Development (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")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 |
Details
| biocViews | RNASeq, SequenceMatching, Sequencing, Software |
| Version | 0.99.4 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| 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 |
| 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_0.99.4.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | posDemux_0.99.4.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 |