cigarillo
This is the released version of cigarillo; for the devel version, see cigarillo.
Efficient manipulation of CIGAR strings
Bioconductor version: Release (3.23)
CIGAR stands for Concise Idiosyncratic Gapped Alignment Report. CIGAR strings are found in the BAM files produced by most aligners and in the AIRR-formatted output produced by IgBLAST. The cigarillo package provides functions to parse and inspect CIGAR strings, trim them, turn them into ranges of positions relative to the "query space" or "reference space", and project positions or sequences from one space to the other. Note that these operations are low-level operations that the user rarely needs to perform directly. More typically, they are performed behind the scene by higher-level functionality implemented in other packages like Bioconductor packages GenomicAlignments and igblastr.
Author: Hervé Pagès [aut, cre] 
, Valerie Obenchain [aut], Michael Lawrence [aut], Patrick Aboyoun [ctb], Fedor Bezrukov [ctb], Martin Morgan [ctb]
Maintainer: Hervé Pagès <hpages.on.github at gmail.com>
citation("cigarillo")):Hervé Pagès, Valerie Obenchain, Michael Lawrence. cigarillo: Efficient manipulation of CIGAR strings. doi:10.18129/B9.bioc.cigarillo, R package version 1.2.1, https://bioconductor.org/packages/cigarillo.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("cigarillo")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("cigarillo")| The cigarillo package | HTML | R Script |
| Reference Manual |
Details
| biocViews | Alignment, Infrastructure, SequenceMatching, Sequencing, Software |
| Version | 1.2.1 |
| In Bioconductor since | BioC 3.22 (R-4.5) (1 year) |
| License | Artistic-2.0 |
| Depends | methods, BiocGenerics, S4Vectors (>= 0.47.2), IRanges, Biostrings |
| Imports | stats |
| System Requirements | |
| URL | https://bioconductor.org/packages/cigarillo |
| Bug Reports | https://github.com/Bioconductor/cigarillo/issues |
See More
| Suggests | Rsamtools, GenomicAlignments, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, testthat, knitr, rmarkdown, BiocStyle |
| Linking To | S4Vectors, IRanges |
| Enhances | |
| Depends On Me | |
| Imports Me | GenomicAlignments |
| Suggests Me | alakazam |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | cigarillo_1.2.1.tar.gz |
| Windows Binary (x86_64) | cigarillo_1.2.1.zip |
| macOS Binary (big-sur-x86_64) | cigarillo_1.2.1.tgz |
| macOS Binary (sonoma-arm64) | cigarillo_1.2.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cigarillo |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cigarillo |
| Package Short Url | https://bioconductor.org/packages/cigarillo/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.23 | Source Archive |