cigarillo
This is the development version of cigarillo; to use it, please install the devel version of Bioconductor.
Efficient manipulation of CIGAR strings
Bioconductor version: Development (3.22)
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")):
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("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 | 0.99.1 |
| In Bioconductor since | BioC 3.22 (R-4.5) |
| 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 | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | cigarillo_0.99.1.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | cigarillo_0.99.1.tgz |
| macOS Binary (arm64) | cigarillo_0.99.1.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/cigarillo |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/cigarillo |
| Bioc Package Browser | https://code.bioconductor.org/browse/cigarillo/ |
| Package Short Url | https://bioconductor.org/packages/cigarillo/ |
| Package Downloads Report | Download Stats |