:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-bcseq' .. highlight: bash bioconductor-bcseq ================== .. conda:recipe:: bioconductor-bcseq :replaces_section_title: :noindex: Fast Sequence Mapping in High\-Throughput shRNA and CRISPR Screens :homepage: https://bioconductor.org/packages/3.18/bioc/html/bcSeq.html :license: GPL (>= 2) :recipe: /`bioconductor-bcseq `_/`meta.yaml `_ This Rcpp\-based package implements a highly efficient data structure and algorithm for performing alignment of short reads from CRISPR or shRNA screens to reference barcode library. Sequencing error are considered and matching qualities are evaluated based on Phred scores. A Bayes\' classifier is employed to predict the originating barcode of a read. The package supports provision of user\-defined probability models for evaluating matching qualities. The package also supports multi\-threading. .. conda:package:: bioconductor-bcseq |downloads_bioconductor-bcseq| |docker_bioconductor-bcseq| :versions: .. raw:: html
1.24.0-01.22.0-01.20.0-11.20.0-01.16.0-21.16.0-11.16.0-01.14.0-01.12.0-1 ``1.24.0-0``,  ``1.22.0-0``,  ``1.20.0-1``,  ``1.20.0-0``,  ``1.16.0-2``,  ``1.16.0-1``,  ``1.16.0-0``,  ``1.14.0-0``,  ``1.12.0-1``,  ``1.12.0-0``,  ``1.10.0-0``,  ``1.8.0-0``,  ``1.6.0-1``,  ``1.4.0-0`` .. raw:: html
:depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :depends bioconductor-biostrings: ``>=2.70.1,<2.71.0a0`` :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-matrix: :depends r-rcpp: ``>=0.12.12`` :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-bcseq and update with:: mamba update bioconductor-bcseq To create a new environment, run:: mamba create --name myenvname bioconductor-bcseq 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-bcseq: (see `bioconductor-bcseq/tags`_ for valid values for ````) .. |downloads_bioconductor-bcseq| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-bcseq.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-bcseq :alt: (downloads) .. |docker_bioconductor-bcseq| image:: https://quay.io/repository/biocontainers/bioconductor-bcseq/status :target: https://quay.io/repository/biocontainers/bioconductor-bcseq .. _`bioconductor-bcseq/tags`: https://quay.io/repository/biocontainers/bioconductor-bcseq?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-bcseq/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-bcseq/README.html