:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'fba' .. highlight: bash fba === .. conda:recipe:: fba :replaces_section_title: :noindex: Tools for single\-cell feature barcoding analysis. Citation\: Duan\, et al \(2021\) \. :homepage: https://github.com/jlduan/fba :documentation: https://jlduan.github.io/fba :license: MIT :recipe: /`fba `_/`meta.yaml `_ \'fba is a flexible and streamlined toolbox for quality control\, quantification\, demultiplexing of various single\-cell feature barcoding assays. It can be applied to customized feature barcoding specifications\, including different CRISPR constructs or targeted enriched transcripts. fba allows users to customize a wide range of parameters for the quantification and demultiplexing process. fba also has a user\-friendly quality control module\, which is helpful in troubleshooting feature barcoding experiments.\' .. conda:package:: fba |downloads_fba| |docker_fba| :versions: ``0.0.13-0``,  ``0.0.12-0``,  ``0.0.11-0``,  ``0.0.10.post1-0`` :depends dnaio: ``>=0.10.0`` :depends hdbscan: ``>=0.8.21`` :depends matplotlib-base: ``>=3.3`` :depends numpy: ``>=1.19.0`` :depends pandas: ``>=1.0.0`` :depends polyleven: ``>=0.5`` :depends pyclustering: ``>=0.10.1`` :depends pysam: ``>=0.14.0`` :depends python: ``>=3.6`` :depends regex: :depends scikit-learn: ``>=0.23.0`` :depends scipy: ``>=1.5.0`` :depends seaborn: ``>=0.10.0`` :depends statsmodels: ``>=0.11.1`` :depends umap-learn: :depends umi_tools: ``>=1.0.0`` :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 fba and update with:: mamba update fba To create a new environment, run:: mamba create --name myenvname fba 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/fba: (see `fba/tags`_ for valid values for ````) .. |downloads_fba| image:: https://img.shields.io/conda/dn/bioconda/fba.svg?style=flat :target: https://anaconda.org/bioconda/fba :alt: (downloads) .. |docker_fba| image:: https://quay.io/repository/biocontainers/fba/status :target: https://quay.io/repository/biocontainers/fba .. _`fba/tags`: https://quay.io/repository/biocontainers/fba?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/fba/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/fba/README.html