fRagmentomics
This is the development version of fRagmentomics; to use it, please install the devel version of Bioconductor.
Extract Fragmentomics Features and Mutational Status
Bioconductor version: Development (3.23)
A user-friendly R package that enables the characterization of each cfDNA fragment overlapping one or multiple mutations of interest, starting from a sequencing file containing aligned reads (BAM file). fRagmentomics supports multiple mutation input formats (e.g., VCF, TSV, or string "chr:pos:ref:alt" representation), accommodates one-based and zero-based genomic conventions, handles mutation representation ambiguities, and accepts any reference file and species in FASTA format. For each cfDNA fragment, fRagmentomics outputs its size, its 3' and 5' sequences, and its mutational status. Optionally, when users set apply_bcftools_norm = TRUE, fRagmentomics invokes the external command-line tool bcftools norm to left-align and normalize variants. If bcftools is not found on the system PATH while this option is enabled, the function errors. The package does not install external software; see the INSTALL file for per-OS instructions.
Author: Killian Maudet [aut, cre]
, Yoann Pradat [aut]
, Juliette Samaniego [aut], Elsa Bernard [aut]
Maintainer: Killian Maudet <killian.maudet at gustaveroussy.fr>
citation("fRagmentomics")):
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("fRagmentomics")
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("fRagmentomics")| A Per-Fragment Analysis Workflow | HTML | R Script |
| Reference Manual |
Details
| biocViews | Alignment, DNASeq, Genetics, IndelDetection, MultipleSequenceAlignment, Sequencing, Software, VariantDetection |
| Version | 0.99.11 |
| In Bioconductor since | BioC 3.23 (R-4.6) |
| License | GPL (>= 3) |
| Depends | R (>= 4.1.0) |
| Imports | Biostrings, data.table, dplyr, future, future.apply, GenomeInfoDb, GenomicRanges, ggh4x, ggplot2, ggseqlogo, IRanges, purrr, RColorBrewer, readr, rlang, Rsamtools(>= 2.4.0), S4Vectors, VariantAnnotation, scales, stringr, tibble, tidyr |
| System Requirements | (optional) bcftools (>= 1.21) for VCF left-alignment/normalization via 'bcftools norm' |
| URL | https://github.com/ElsaB-Lab/fRagmentomics |
| Bug Reports | https://github.com/ElsaB-Lab/fRagmentomics/issues |
See More
| Suggests | ragg, covr, testthat (>= 3.0.0), knitr, rmarkdown (>= 1.14), BiocStyle |
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| Depends On Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | fRagmentomics_0.99.11.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (big-sur-arm64) | fRagmentomics_0.99.11.tgz |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/fRagmentomics |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/fRagmentomics |
| Bioc Package Browser | https://code.bioconductor.org/browse/fRagmentomics/ |
| Package Short Url | https://bioconductor.org/packages/fRagmentomics/ |
| Package Downloads Report | Download Stats |