Package Recipe 'bioconductor-debrowser'

recipe bioconductor-debrowser

Interactive Differential Expresion Analysis Browser

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/debrowser.html
License:: GPL-3 + file LICENSE
Recipe:: /bioconductor-debrowser/meta.yaml

Bioinformatics platform containing interactive plots and tables for differential gene and region expression studies. Allows visualizing expression data much more deeply in an interactive and faster way. By changing the parameters, users can easily discover different parts of the data that like never have been done before. Manually creating and looking these plots takes time. With DEBrowser users can prepare plots without writing any code. Differential expression, PCA and clustering analysis are made on site and the results are shown in various plots such as scatter, bar, box, volcano, ma plots and Heatmaps.

package bioconductor-debrowser¶

Versions:

1.38.0-0, 1.34.0-0, 1.30.0-0, 1.28.2-0, 1.26.0-0, 1.22.1-0, 1.20.0-0, 1.18.2-0, 1.18.0-0,

1.38.0-0, 1.34.0-0, 1.30.0-0, 1.28.2-0, 1.26.0-0, 1.22.1-0, 1.20.0-0, 1.18.2-0, 1.18.0-0, 1.16.0-0, 1.14.0-0, 1.12.2-0

Depends:

on bioconductor-annotate >=1.88.0,<1.89.0
on bioconductor-annotationdbi >=1.72.0,<1.73.0
on bioconductor-apeglm >=1.32.0,<1.33.0
on bioconductor-clusterprofiler >=4.18.0,<4.19.0
on bioconductor-deseq2 >=1.50.0,<1.51.0
on bioconductor-dose >=4.4.0,<4.5.0
on bioconductor-edger >=4.8.0,<4.9.0
on bioconductor-enrichplot >=1.30.0,<1.31.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-harman >=1.38.0,<1.39.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-org.hs.eg.db >=3.22.0,<3.23.0
on bioconductor-org.mm.eg.db >=3.22.0,<3.23.0
on bioconductor-pathview >=1.50.0,<1.51.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-sva >=3.58.0,<3.59.0
on r-ashr
on r-base >=4.5,<4.6.0a0
on r-colourpicker
on r-dt
on r-ggplot2
on r-gplots
on r-heatmaply
on r-igraph
on r-jsonlite
on r-plotly
on r-rcolorbrewer
on r-rcurl
on r-reshape2
on r-shiny
on r-shinybs
on r-shinydashboard
on r-shinyjs
on r-stringi

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-debrowser

to add into an existing workspace instead, run:

pixi add bioconductor-debrowser

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-debrowser

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-debrowser

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

docker pull quay.io/biocontainers/bioconductor-debrowser:<tag>

(see bioconductor-debrowser/tags for valid values for <tag>).

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an 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-debrowser/README.html)