fRagmentomics
Extract Fragmentomics Features and Mutational Status
Bioconductor version: 3.23 · Package version: 1.0.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("fRagmentomics")Details
| Maintainer | Killian Maudet <killian.maudet@gustaveroussy.fr> |
| Author | Killian Maudet [aut, cre] (ORCID: <https://orcid.org/0009-0003-3237-092X>), Juliette Samaniego [aut] (ORCID: <https://orcid.org/0009-0002-3421-1810>), Yoann Pradat [aut] (ORCID: <https://orcid.org/0000-0002-4647-5779>), Elsa Bernard [aut] (ORCID: <https://orcid.org/0000-0002-2057-7187>) |
| License | GPL (>= 3) |
| URL | https://github.com/ElsaB-Lab/fRagmentomics |
| Bug Reports | https://github.com/ElsaB-Lab/fRagmentomics/issues |
| System Requirements | (optional) bcftools (>= 1.21) for VCF left-alignment/normalization via 'bcftools norm' |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Alignment, DNASeq, Genetics, IndelDetection, MultipleSequenceAlignment, Sequencing, Software, VariantDetection |
| Package Short Url | https://bioconductor.org/packages/fRagmentomics/ |
Citation
From within R, enter citation("fRagmentomics"):
Killian Maudet, Juliette Samaniego, Yoann Pradat, Elsa Bernard. fRagmentomics: Extract Fragmentomics Features and Mutational Status. doi:10.18129/B9.bioc.fRagmentomics, R package version 1.0.0, https://bioconductor.org/packages/fRagmentomics.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | fRagmentomics_1.0.0.tar.gz |
| Windows binary (x86_64) | fRagmentomics_1.0.0.zip |
| macOS binary (arm64) | fRagmentomics_1.0.0.tgz |
| macOS binary (x86_64) | fRagmentomics_1.0.0.tgz |
Dependencies
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
Suggests: ragg, covr, testthat (>= 3.0.0), knitr, rmarkdown (>= 1.14), BiocStyle