Package: SimFFPE
Type: Package
Title: NGS Read Simulator for FFPE Tissue
Version: 1.25.0
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
Config/pak/sysreqs: libbz2-dev liblzma-dev xz-utils zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-04-28 12:51:42 UTC
RemoteUrl: https://github.com/bioc/SimFFPE
RemoteRef: HEAD
RemoteSha: f626f0c8b81c05c473e6a58efe62c23ff80aad4f
NeedsCompilation: no
Packaged: 2026-07-04 06:14:12 UTC; root
Author: Lanying Wei [aut, cre] (ORCID: <https://orcid.org/0000-0002-4281-8017>)
Maintainer: Lanying Wei <lanying.wei@uni-muenster.de>