SimFFPE
This is the development version of SimFFPE; for the stable release version, see SimFFPE.
NGS Read Simulator for FFPE Tissue
Bioconductor version: Development (3.24)
The NGS (Next-Generation Sequencing) reads from FFPE (Formalin-Fixed Paraffin-Embedded) samples contain numerous artifact chimeric reads (ACRS), which can lead to false positive structural variant calls. These ACRs are derived from the combination of two single-stranded DNA (ss-DNA) fragments with short reverse complementary regions (SRCRs). This package simulates these artifact chimeric reads as well as normal reads for FFPE samples on the whole genome / several chromosomes / large regions.
Author: Lanying Wei [aut, cre]
Maintainer: Lanying Wei <lanying.wei at uni-muenster.de>
citation("SimFFPE")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("SimFFPE")
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("SimFFPE")| An introduction to SimFFPE | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | Alignment, DataImport, MultipleComparison, SequenceMatching, Sequencing, Software |
| Version | 1.25.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | LGPL-3 |
| Depends | Biostrings |
| Imports | dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges, Rsamtools, parallel, graphics, stats, utils, methods |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle |
| Linking To | |
| 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 | SimFFPE_1.25.0.tar.gz |
| Windows Binary (x86_64) | SimFFPE_1.25.0.zip |
| macOS Binary (big-sur-x86_64) | SimFFPE_1.25.0.tgz |
| macOS Binary (sonoma-arm64) | SimFFPE_1.25.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SimFFPE |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SimFFPE |
| Bioc Package Browser | https://code.bioconductor.org/browse/SimFFPE/ |
| Package Short Url | https://bioconductor.org/packages/SimFFPE/ |
| Package Downloads Report | Download Stats |