:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'mimseq' .. highlight: bash mimseq ====== .. conda:recipe:: mimseq :replaces_section_title: :noindex: Modification\-induced misincorporation tRNA sequencing. :homepage: https://github.com/nedialkova-lab/mim-tRNAseq :license: GPL3 / GPL-3.0-only :recipe: /`mimseq `_/`meta.yaml `_ .. conda:package:: mimseq |downloads_mimseq| |docker_mimseq| :versions: .. raw:: html
1.3.8-01.3.7-01.3.6-11.3.6-01.3.5-01.3.4-01.3.3-01.3.2-01.3-0 ``1.3.8-0``,  ``1.3.7-0``,  ``1.3.6-1``,  ``1.3.6-0``,  ``1.3.5-0``,  ``1.3.4-0``,  ``1.3.3-0``,  ``1.3.2-0``,  ``1.3-0``,  ``1.2.1-0``,  ``1.2-0``,  ``1.1.7-0``,  ``1.1.6-0``,  ``1.1.4-0``,  ``1.1.2-0``,  ``1.1.1-0``,  ``1.1-0``,  ``1.0.3-0``,  ``1.0.2-0``,  ``1.0.1-0``,  ``1.0-0``,  ``0.4-0``,  ``0.3.4.9-0``,  ``0.3.4.8-0``,  ``0.3.4.7-0``,  ``0.3.4.5-0``,  ``0.3.4.3-0``,  ``0.3.4.1-0``,  ``0.3.4-0``,  ``0.3.3.2-0``,  ``0.3.3-0``,  ``0.3.2-0``,  ``0.3.1-0``,  ``0.2.6-0``,  ``0.2.5.6-0``,  ``0.2.5.5-1``,  ``0.2.5.5-0``,  ``0.2.5.4-0``,  ``0.2.5.3-0`` .. raw:: html
:depends bedtools: ``>=2.30.0`` :depends bioconductor-complexheatmap: ``>=2.2.0`` :depends bioconductor-deseq2: ``>=1.26.0`` :depends biopython: ``>=1.79`` :depends blast: ``>=2.10.1`` :depends gmap: ``<=2019.02.26`` :depends infernal: ``>=1.1.4`` :depends matplotlib-base: ``>=3.4.2`` :depends numpy: ``>=1.21.1`` :depends pandas: ``>=1.3.1`` :depends pybedtools: ``>=0.8.2`` :depends pyfiglet: ``>=0.8.post1`` :depends pysam: ``>=0.16.0.1`` :depends python: ``3.7.*`` :depends r-base: ``>=4.1`` :depends r-calibrate: ``>=1.7.7`` :depends r-devtools: ``>=2.4.1`` :depends r-dplyr: ``>=1.0.6`` :depends r-ggplot2: ``>=3.3.5`` :depends r-ggpol: ``>=0.0.7`` :depends r-gridextra: ``>=2.3`` :depends r-pheatmap: ``>=1.0.12`` :depends r-plyr: ``>=1.8.6`` :depends r-reshape2: ``>=1.4.4`` :depends r-tidyverse: ``>=1.3.0`` :depends requests: ``>=2.26.0`` :depends samtools: ``>=1.11`` :depends seaborn-base: ``>=0.11.1`` :depends statsmodels: ``>=0.13.1`` :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 mimseq and update with:: mamba update mimseq To create a new environment, run:: mamba create --name myenvname mimseq 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/mimseq: (see `mimseq/tags`_ for valid values for ````) .. |downloads_mimseq| image:: https://img.shields.io/conda/dn/bioconda/mimseq.svg?style=flat :target: https://anaconda.org/bioconda/mimseq :alt: (downloads) .. |docker_mimseq| image:: https://quay.io/repository/biocontainers/mimseq/status :target: https://quay.io/repository/biocontainers/mimseq .. _`mimseq/tags`: https://quay.io/repository/biocontainers/mimseq?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/mimseq/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/mimseq/README.html