Package Recipe 'bioconductor-batchqc'

recipe bioconductor-batchqc

Batch Effects Quality Control Software

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/BatchQC.html
License:: MIT + file LICENSE
Recipe:: /bioconductor-batchqc/meta.yaml
Links:: biotools: batchqc

Sequencing and microarray samples often are collected or processed in multiple batches or at different times. This often produces technical biases that can lead to incorrect results in the downstream analysis. BatchQC is a software tool that streamlines batch preprocessing and evaluation by providing interactive diagnostics, visualizations, and statistical analyses to explore the extent to which batch variation impacts the data. BatchQC diagnostics help determine whether batch adjustment needs to be done, and how correction should be applied before proceeding with a downstream analysis. Moreover, BatchQC interactively applies multiple common batch effect approaches to the data and the user can quickly see the benefits of each method. BatchQC is developed as a Shiny App. The output is organized into multiple tabs and each tab features an important part of the batch effect analysis and visualization of the data. The BatchQC interface has the following analysis groups: Summary, Differential Expression, Median Correlations, Heatmaps, Circular Dendrogram, PCA Analysis, Shape, ComBat and SVA.

package bioconductor-batchqc¶

Versions:

2.6.1-0, 2.6.0-0, 2.2.0-0, 1.30.0-0, 1.28.0-0, 1.26.0-0, 1.22.0-0, 1.20.0-0, 1.18.0-1,

2.6.1-0, 2.6.0-0, 2.2.0-0, 1.30.0-0, 1.28.0-0, 1.26.0-0, 1.22.0-0, 1.20.0-0, 1.18.0-1, 1.18.0-0, 1.16.0-0, 1.14.0-0, 1.12.0-1, 1.10.1-0, 1.8.1-0, 1.6.1-0

Depends:

on bioconductor-deseq2 >=1.50.0,<1.51.0
on bioconductor-ebseq >=2.8.0,<2.9.0
on bioconductor-edger >=4.8.0,<4.9.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-scran >=1.38.0,<1.39.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-sva >=3.58.0,<3.59.0
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-dplyr
on r-fnn
on r-ggdendro
on r-ggnewscale
on r-ggplot2
on r-mass
on r-matrixstats
on r-pheatmap
on r-rcolorbrewer
on r-reader
on r-reshape2
on r-shiny
on r-shinyjs
on r-shinythemes
on r-tibble
on r-tidyr
on r-tidyverse
on r-umap

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-batchqc

to add into an existing workspace instead, run:

pixi add bioconductor-batchqc

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-batchqc

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-batchqc

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-batchqc:<tag>

(see bioconductor-batchqc/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-batchqc/README.html)