SimFFPE
This is the development version of SimFFPE; for the stable release version, see SimFFPE.
NGS Read Simulator for FFPE Tissue
Bioconductor version: Development (3.21)
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] (ORCID:
Maintainer: Lanying Wei <lanying.wei at uni-muenster.de>
citation("SimFFPE")):
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("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 | 1.19.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (4.5 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_1.19.0.tar.gz |
| Windows Binary (x86_64) | SimFFPE_1.19.0.zip |
| macOS Binary (x86_64) | SimFFPE_1.19.0.tgz |
| macOS Binary (arm64) | SimFFPE_1.19.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SimFFPE |
| Source Repository (Developer Access) | git clone [email protected]:packages/SimFFPE |
| Bioc Package Browser | https://code.bioconductor.org/browse/SimFFPE/ |
| Package Short Url | https://bioconductor.org/packages/SimFFPE/ |
| Package Downloads Report | Download Stats |