amplican
Automated analysis of CRISPR experiments
Bioconductor version: 3.23 · Package version: 1.34.0
`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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("amplican")Details
| Maintainer | Eivind Valen <eivind.valen@gmail.com> |
| Author | Kornel Labun [aut], Eivind Valen [cph, cre] |
| License | GPL-3 |
| URL | https://github.com/valenlab/amplican |
| Bug Reports | https://github.com/valenlab/amplican/issues |
| Downloads rank | 445 |
| Source branch | RELEASE_3_23 |
| biocViews | Alignment, CRISPR, ImmunoOncology, Software, Technology, qPCR |
Documentation
- ampliCan FAQ
- ampliCan Overview
- Report breakdown by amplicon sequence
- Report breakdown by barcode
- Report breakdown by group
- Report breakdown by guideRNA
- Report breakdown by ID
- Summary Read Report
Download
Dependencies
Depends: R (>= 3.5.0), methods, BiocGenerics (>= 0.22.0), Biostrings (>= 2.44.2), pwalign
Imports: Rcpp, utils (>= 3.4.1), S4Vectors (>= 0.14.3), ShortRead (>= 1.34.0), IRanges (>= 2.10.2), GenomicRanges (>= 1.61.1), Seqinfo, BiocParallel (>= 1.10.1), gtable (>= 0.2.0), gridExtra (>= 2.2.1), ggplot2 (>= 3.3.4), ggthemes (>= 3.4.0), stringr (>= 1.2.0), stats (>= 3.4.1), matrixStats (>= 0.52.2), Matrix (>= 1.2-10), data.table (>= 1.10.4-3), rmarkdown (>= 1.6), knitr (>= 1.16), cluster (>= 2.1.4), rlang (>= 1.2.0)
LinkingTo: Rcpp
Suggests: testthat, BiocStyle, GenomicAlignments