Bioconductor version: Release (3.6)
`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 (from within R,
enter citation("amplican")
):
To install this package, start R and enter:
## try http:// if https:// URLs are not supported source("https://bioconductor.org/biocLite.R") biocLite("amplican")
HTML | R Script | 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 |
Reference Manual | ||
Text | NEWS |
biocViews | Alignment, CRISPR, Software, Technology, qPCR |
Version | 1.0.0 |
License | GPL-3 |
Depends | R (>= 3.4.0), methods, BiocGenerics(>= 0.22.0), Biostrings(>= 2.44.2), data.table (>= 1.10.4) |
Imports | 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 (>= 2.2.0), ggbio(>= 1.24.1), 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), clusterCrit (>= 1.2.7) |
LinkingTo | |
Suggests | testthat, BiocStyle |
SystemRequirements | |
Enhances | |
URL | https://github.com/valenlab/amplican |
BugReports | https://github.com/valenlab/amplican/issues |
Depends On Me | |
Imports Me | |
Suggests Me | |
Build Report |
Follow Installation instructions to use this package in your R session.
Source Package | amplican_1.0.0.tar.gz |
Windows Binary | amplican_1.0.0.zip |
Mac OS X 10.11 (El Capitan) | amplican_1.0.0.tgz |
Source Repository | git clone https://git.bioconductor.org/packages/amplican |
Package Short Url | http://bioconductor.org/packages/amplican/ |
Package Downloads Report | Download Stats |
Documentation »
Bioconductor
R / CRAN packages and documentation
Support »
Please read the posting guide. Post questions about Bioconductor to one of the following locations: