:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-simffpe' .. highlight: bash bioconductor-simffpe ==================== .. conda:recipe:: bioconductor-simffpe :replaces_section_title: :noindex: NGS Read Simulator for FFPE Tissue :homepage: https://bioconductor.org/packages/3.18/bioc/html/SimFFPE.html :license: LGPL-3 :recipe: /`bioconductor-simffpe `_/`meta.yaml `_ 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. .. conda:package:: bioconductor-simffpe |downloads_bioconductor-simffpe| |docker_bioconductor-simffpe| :versions: ``1.14.0-0``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.0-1``,  ``1.2.0-0``,  ``1.0.0-0`` :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-doparallel: :depends r-dplyr: :depends r-foreach: :depends r-truncnorm: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`set-up-channels`). While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see `here `_ for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others. Given that you already have a conda environment in which you want to have this package, install with:: mamba install bioconductor-simffpe and update with:: mamba update bioconductor-simffpe To create a new environment, run:: mamba create --name myenvname bioconductor-simffpe with ``myenvname`` being a reasonable name for the environment (see e.g. the `mamba docs `_ for details and further options). Alternatively, use the docker container:: docker pull quay.io/biocontainers/bioconductor-simffpe: (see `bioconductor-simffpe/tags`_ for valid values for ````) .. |downloads_bioconductor-simffpe| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-simffpe.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-simffpe :alt: (downloads) .. |docker_bioconductor-simffpe| image:: https://quay.io/repository/biocontainers/bioconductor-simffpe/status :target: https://quay.io/repository/biocontainers/bioconductor-simffpe .. _`bioconductor-simffpe/tags`: https://quay.io/repository/biocontainers/bioconductor-simffpe?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-simffpe/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-simffpe/README.html