:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-srnadiff' .. highlight: bash bioconductor-srnadiff ===================== .. conda:recipe:: bioconductor-srnadiff :replaces_section_title: :noindex: Finding differentially expressed unannotated genomic regions from RNA\-seq data :homepage: https://bioconductor.org/packages/3.18/bioc/html/srnadiff.html :license: GPL-3 :recipe: /`bioconductor-srnadiff `_/`meta.yaml `_ srnadiff is a package that finds differently expressed regions from RNA\-seq data at base\-resolution level without relying on existing annotation. To do so\, the package implements the identify\-then\-annotate methodology that builds on the idea of combining two pipelines approachs differential expressed regions detection and differential expression quantification. It reads BAM files as input\, and outputs a list differentially regions\, together with the adjusted p\-values. .. conda:package:: bioconductor-srnadiff |downloads_bioconductor-srnadiff| |docker_bioconductor-srnadiff| :versions: .. raw:: html
1.22.0-01.18.0-11.18.0-01.14.0-21.14.0-11.14.0-01.12.2-01.11.0-01.10.1-0 ``1.22.0-0``,  ``1.18.0-1``,  ``1.18.0-0``,  ``1.14.0-2``,  ``1.14.0-1``,  ``1.14.0-0``,  ``1.12.2-0``,  ``1.11.0-0``,  ``1.10.1-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-0``,  ``1.4.0-1``,  ``1.2.0-0`` .. raw:: html
:depends bioconductor-bayseq: ``>=2.36.0,<2.37.0`` :depends bioconductor-bayseq: ``>=2.36.0,<2.37.0a0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0`` :depends bioconductor-biocparallel: ``>=1.36.0,<1.37.0a0`` :depends bioconductor-biocstyle: ``>=2.30.0,<2.31.0`` :depends bioconductor-biocstyle: ``>=2.30.0,<2.31.0a0`` :depends bioconductor-deseq2: ``>=1.42.0,<1.43.0`` :depends bioconductor-deseq2: ``>=1.42.0,<1.43.0a0`` :depends bioconductor-edger: ``>=4.0.0,<4.1.0`` :depends bioconductor-edger: ``>=4.0.2,<4.1.0a0`` :depends bioconductor-genomeinfodb: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomeinfodb: ``>=1.38.1,<1.39.0a0`` :depends bioconductor-genomicalignments: ``>=1.38.0,<1.39.0`` :depends bioconductor-genomicalignments: ``>=1.38.0,<1.39.0a0`` :depends bioconductor-genomicfeatures: ``>=1.54.0,<1.55.0`` :depends bioconductor-genomicfeatures: ``>=1.54.1,<1.55.0a0`` :depends bioconductor-genomicranges: ``>=1.54.0,<1.55.0`` :depends bioconductor-genomicranges: ``>=1.54.1,<1.55.0a0`` :depends bioconductor-gviz: ``>=1.46.0,<1.47.0`` :depends bioconductor-gviz: ``>=1.46.1,<1.47.0a0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0`` :depends bioconductor-iranges: ``>=2.36.0,<2.37.0a0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0`` :depends bioconductor-rsamtools: ``>=2.18.0,<2.19.0a0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0`` :depends bioconductor-rtracklayer: ``>=1.62.0,<1.63.0a0`` :depends bioconductor-s4vectors: ``>=0.40.0,<0.41.0`` :depends bioconductor-s4vectors: ``>=0.40.2,<0.41.0a0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0`` :depends bioconductor-summarizedexperiment: ``>=1.32.0,<1.33.0a0`` :depends libblas: ``>=3.9.0,<4.0a0`` :depends libgcc-ng: ``>=12`` :depends liblapack: ``>=3.9.0,<4.0a0`` :depends libstdcxx-ng: ``>=12`` :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-biocmanager: :depends r-devtools: :depends r-rcpp: ``>=0.12.8`` :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-srnadiff and update with:: mamba update bioconductor-srnadiff To create a new environment, run:: mamba create --name myenvname bioconductor-srnadiff 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-srnadiff: (see `bioconductor-srnadiff/tags`_ for valid values for ````) .. |downloads_bioconductor-srnadiff| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-srnadiff.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-srnadiff :alt: (downloads) .. |docker_bioconductor-srnadiff| image:: https://quay.io/repository/biocontainers/bioconductor-srnadiff/status :target: https://quay.io/repository/biocontainers/bioconductor-srnadiff .. _`bioconductor-srnadiff/tags`: https://quay.io/repository/biocontainers/bioconductor-srnadiff?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-srnadiff/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-srnadiff/README.html