Package: SimFFPE
Type: Package
Title: NGS Read Simulator for FFPE Tissue
Version: 1.23.0
Authors@R: person("Lanying", "Wei", email="lanying.wei@uni-muenster.de",
    role = c("aut", "cre"), comment = c(ORCID = "0000-0002-4281-8017"))
Description: 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.
License: LGPL-3
Encoding: UTF-8
Depends: Biostrings
Imports: dplyr, foreach, doParallel, truncnorm, GenomicRanges, IRanges, Rsamtools, parallel, graphics, stats, utils, methods
Suggests: BiocStyle
biocViews: Sequencing, Alignment, MultipleComparison, SequenceMatching, DataImport
git_url: https://git.bioconductor.org/packages/SimFFPE
git_branch: devel
git_last_commit: daeddda
git_last_commit_date: 2025-10-29
Repository: Bioconductor 3.23
