:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-exomepeak2' .. highlight: bash bioconductor-exomepeak2 ======================= .. conda:recipe:: bioconductor-exomepeak2 :replaces_section_title: :noindex: Bias\-aware Peak Calling and Quantification for MeRIP\-Seq :homepage: https://bioconductor.org/packages/3.14/bioc/html/exomePeak2.html :license: GPL (>= 2) :recipe: /`bioconductor-exomepeak2 `_/`meta.yaml `_ exomePeak2 provides bias\-aware quantification and peak detection for Methylated RNA immunoprecipitation sequencing data \(MeRIP\-Seq\). MeRIP\-Seq is a commonly applied sequencing technology that can measure the location and abundance of RNA modification sites under given cell line conditions. However\, quantification and peak calling in MeRIP\-Seq are sensitive to PCR amplification biases\, which generally present in next\-generation sequencing \(NGS\) technologies. In addition\, the count data generated by RNA\-Seq exhibits significant biological variations between biological replicates. exomePeak2 collectively address the challenges by introducing a series of robust data science tools tailored for MeRIP\-Seq. Using exomePeak2\, users can perform peak calling\, modification site quantification and differential analysis through a straightforward single\-step function. Alternatively\, multi\-step functions can be used to generate diagnostic plots and perform customized analyses. .. conda:package:: bioconductor-exomepeak2 |downloads_bioconductor-exomepeak2| |docker_bioconductor-exomepeak2| :versions: ``1.6.0-0``,  ``1.4.0-0``,  ``1.2.0-1``,  ``1.2.0-0``,  ``1.0.0-0`` :depends bioconductor-apeglm: ``>=1.16.0,<1.17.0`` :depends bioconductor-biobase: ``>=2.54.0,<2.55.0`` :depends bioconductor-biocgenerics: ``>=0.40.0,<0.41.0`` :depends bioconductor-biocparallel: ``>=1.28.0,<1.29.0`` :depends bioconductor-biostrings: ``>=2.62.0,<2.63.0`` :depends bioconductor-bsgenome: ``>=1.62.0,<1.63.0`` :depends bioconductor-cqn: ``>=1.40.0,<1.41.0`` :depends bioconductor-deseq2: ``>=1.34.0,<1.35.0`` :depends bioconductor-genefilter: ``>=1.76.0,<1.77.0`` :depends bioconductor-genomeinfodb: ``>=1.30.0,<1.31.0`` :depends bioconductor-genomicalignments: ``>=1.30.0,<1.31.0`` :depends bioconductor-genomicfeatures: ``>=1.46.0,<1.47.0`` :depends bioconductor-genomicranges: ``>=1.46.0,<1.47.0`` :depends bioconductor-iranges: ``>=2.28.0,<2.29.0`` :depends bioconductor-rsamtools: ``>=2.10.0,<2.11.0`` :depends bioconductor-rtracklayer: ``>=1.54.0,<1.55.0`` :depends bioconductor-s4vectors: ``>=0.32.0,<0.33.0`` :depends bioconductor-summarizedexperiment: ``>=1.24.0,<1.25.0`` :depends r-base: ``>=4.1,<4.2.0a0`` :depends r-ggplot2: :depends r-mclust: :depends r-reshape2: :requirements: .. rubric:: Installation With an activated Bioconda channel (see :ref:`set-up-channels`), install with:: conda install bioconductor-exomepeak2 and update with:: conda update bioconductor-exomepeak2 or use the docker container:: docker pull quay.io/biocontainers/bioconductor-exomepeak2: (see `bioconductor-exomepeak2/tags`_ for valid values for ````) .. |downloads_bioconductor-exomepeak2| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-exomepeak2.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-exomepeak2 :alt: (downloads) .. |docker_bioconductor-exomepeak2| image:: https://quay.io/repository/biocontainers/bioconductor-exomepeak2/status :target: https://quay.io/repository/biocontainers/bioconductor-exomepeak2 .. _`bioconductor-exomepeak2/tags`: https://quay.io/repository/biocontainers/bioconductor-exomepeak2?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-exomepeak2/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-exomepeak2/README.html