recipe bioconductor-sangeranalyser

sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R

Homepage:

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

License:

GPL-2

Recipe:

/bioconductor-sangeranalyser/meta.yaml

This package builds on sangerseqR to allow users to create contigs from collections of Sanger sequencing reads. It provides a wide range of options for a number of commonly-performed actions including read trimming, detecting secondary peaks, and detecting indels using a reference sequence. All parameters can be adjusted interactively either in R or in the associated Shiny applications. There is extensive online documentation, and the package can outputs detailed HTML reports, including chromatograms.

package bioconductor-sangeranalyser

versions:

1.12.0-0,  1.10.0-0,  1.8.0-0,  1.4.0-0,  1.2.0-0,  1.0.0-1,  1.0.0-0

depends bioconductor-biocstyle:

>=2.30.0,<2.31.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-decipher:

>=2.30.0,<2.31.0

depends bioconductor-sangerseqr:

>=1.38.0,<1.39.0

depends r-ape:

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-dt:

depends r-excelr:

depends r-ggdendro:

depends r-gridextra:

depends r-knitr:

>=1.33

depends r-logger:

depends r-openxlsx:

depends r-phangorn:

depends r-plotly:

depends r-reshape2:

depends r-rmarkdown:

>=2.9

depends r-seqinr:

depends r-shiny:

depends r-shinycssloaders:

depends r-shinydashboard:

depends r-shinyjs:

depends r-shinywidgets:

depends r-stringr:

depends r-zeallot:

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-sangeranalyser

and update with::

   mamba update bioconductor-sangeranalyser

To create a new environment, run:

mamba create --name myenvname bioconductor-sangeranalyser

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-sangeranalyser:<tag>

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

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