amplican
This is the development version of amplican; for the stable release version, see amplican.
Automated analysis of CRISPR experiments
Bioconductor version: Development (3.21)
`amplican` performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.
Author: Kornel Labun [aut], Eivind Valen [cph, cre]
Maintainer: Eivind Valen <eivind.valen at gmail.com>
citation("amplican")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("amplican")
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("amplican")| amplican FAQ | HTML | |
| amplican overview | HTML | R Script |
| example amplicon_report report | HTML | R Script |
| example barcode_report report | HTML | R Script |
| example group_report report | HTML | R Script |
| example guide_report report | HTML | R Script |
| example id_report report | HTML | R Script |
| example index report | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, CRISPR, ImmunoOncology, Software, Technology, qPCR |
| Version | 1.29.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (7 years) |
| License | GPL-3 |
| Depends | R (>= 3.5.0), methods, BiocGenerics(>= 0.22.0), Biostrings(>= 2.44.2), pwalign, data.table (>= 1.10.4-3) |
| Imports | Rcpp, utils (>= 3.4.1), S4Vectors(>= 0.14.3), ShortRead(>= 1.34.0), IRanges(>= 2.10.2), GenomicRanges(>= 1.28.4), GenomeInfoDb(>= 1.12.2), BiocParallel(>= 1.10.1), gtable (>= 0.2.0), gridExtra (>= 2.2.1), ggplot2 (>= 3.3.4), ggthemes (>= 3.4.0), waffle (>= 0.7.0), stringr (>= 1.2.0), stats (>= 3.4.1), matrixStats (>= 0.52.2), Matrix (>= 1.2-10), dplyr (>= 0.7.2), rmarkdown (>= 1.6), knitr (>= 1.16), cluster (>= 2.1.4) |
| System Requirements | |
| URL | https://github.com/valenlab/amplican |
| Bug Reports | https://github.com/valenlab/amplican/issues |
See More
| Suggests | testthat, BiocStyle, GenomicAlignments |
| Linking To | Rcpp |
| 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 | amplican_1.29.0.tar.gz |
| Windows Binary (x86_64) | amplican_1.29.0.zip (64-bit only) |
| macOS Binary (x86_64) | amplican_1.29.0.tgz |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/amplican |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/amplican |
| Bioc Package Browser | https://code.bioconductor.org/browse/amplican/ |
| Package Short Url | https://bioconductor.org/packages/amplican/ |
| Package Downloads Report | Download Stats |