- recipe r-bulkanalyser
Given an expression matrix from a bulk sequencing experiment, pre-processes it and creates a shiny app for interactive data analysis and visualisation. The app contains quality checks, differential expression analysis, volcano and cross plots, enrichment analysis and gene regulatory network inference, and can be customised to contain more panels by the user.
- Homepage:
- License:
GPL2 / GPL-2.0-only
- Recipe:
- package r-bulkanalyser¶
- Versions:
1.1.0-3,1.1.0-2,1.1.0-1,1.1.0-0,1.0.0-1,1.0.0-0- Depends:
on bioconductor-complexheatmap
on bioconductor-deseq2
on bioconductor-edger
on bioconductor-genie3
on bioconductor-preprocesscore
on r-base
>=4.4,<4.5.0a0on r-circlize
on r-dplyr
on r-dt
on r-ggforce
on r-ggnewscale
on r-ggplot2
on r-ggrastr
on r-ggrepel
on r-ggvenndiagram
on r-glue
on r-gprofiler2
on r-magrittr
on r-matrixstats
on r-noisyr
on r-rcolorbrewer
on r-rlang
on r-scales
on r-shiny
on r-shinyjqui
on r-shinyjs
on r-shinylp
on r-shinywidgets
on r-stringr
on r-tibble
on r-tidyr
on r-upsetr
on r-visnetwork
- 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 r-bulkanalyser
to add into an existing workspace instead, run:
pixi add r-bulkanalyser
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 r-bulkanalyser
Alternatively, to install into a new environment, run:
conda create -n envname r-bulkanalyser
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/r-bulkanalyser:<tag>
(see r-bulkanalyser/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:
[](http://bioconda.github.io/recipes/r-bulkanalyser/README.html)
