recipe bioconductor-sagenhaft

Collection of functions for reading and comparing SAGE libraries

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/sagenhaft.html

License:

GPL (>= 2)

Recipe:

/bioconductor-sagenhaft/meta.yaml

Links:

biotools: sagenhaft, doi: 10.1038/nmeth.3252

This package implements several functions useful for analysis of gene expression data by sequencing tags as done in SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison. Sequencing error correction is implementing using an Expectation Maximization Algorithm based on a Mixture Model of tag counts.

package bioconductor-sagenhaft

(downloads) docker_bioconductor-sagenhaft

versions:
1.72.0-1,  1.72.0-0,  1.70.0-0,  1.68.0-0,  1.64.0-0,  1.62.0-0,  1.60.0-1,  1.60.0-0,  1.58.0-0, 

1.72.0-1,  1.72.0-0,  1.70.0-0,  1.68.0-0,  1.64.0-0,  1.62.0-0,  1.60.0-1,  1.60.0-0,  1.58.0-0,  1.56.0-0,  1.54.0-1,  1.54.0-0,  1.52.0-0,  1.50.0-0,  1.48.0-0,  1.46.0-0

depends r-base:

>=4.3,<4.4.0a0

depends r-sparsem:

>=0.73

requirements:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see 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-sagenhaft

and update with::

   mamba update bioconductor-sagenhaft

To create a new environment, run:

mamba create --name myenvname bioconductor-sagenhaft

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-sagenhaft:<tag>

(see `bioconductor-sagenhaft/tags`_ for valid values for ``<tag>``)

Download stats

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-sagenhaft/README.html)