posDemux
Positional combinatorial sequence demultiplexer
Bioconductor version: 3.24 · Package version: 1.1.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("posDemux")Details
| Maintainer | Jakob Peder Pettersen <jakobpeder.pettersen@gmail.com> |
| Author | Jakob Peder Pettersen [aut, cre] (ORCID: <https://orcid.org/0000-0002-3485-1634>), Centre for new antibacterial strategies (CANS) [fnd] |
| License | AGPL (>= 3) |
| URL | https://github.com/yaccos/posDemux, https://yaccos.github.io/posDemux/ |
| Bug Reports | https://github.com/yaccos/posDemux/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | RNASeq, SequenceMatching, Sequencing, Software |
| Package Short Url | https://bioconductor.org/packages/posDemux/ |
Citation
From within R, enter citation("posDemux"):
Jakob Peder Pettersen. posDemux: Positional combinatorial sequence demultiplexer. doi:10.18129/B9.bioc.posDemux, R package version 1.1.0, https://bioconductor.org/packages/posDemux.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | posDemux_1.1.0.tar.gz |
| Windows binary (x86_64) | posDemux_1.1.0.zip |
| macOS binary (arm64) | posDemux_1.1.0.tgz |
| macOS binary (x86_64) | posDemux_1.1.0.tgz |
Dependencies
Depends: R (>= 4.5.0)
Imports: Biostrings, ggplot2, methods, assertthat, glue, magrittr, dplyr, rlang, ShortRead, readr, shiny, purrr
LinkingTo: Rcpp, Biostrings, IRanges, S4Vectors, XVector
Suggests: testthat, devtools, DNABarcodes, knitr, rmarkdown, tibble, tidyr, BiocStyle, RefManageR, sessioninfo, DBI, chunked, RSQLite, dbplyr