Package Recipe 'bioconductor-strandcheckr'

recipe bioconductor-strandcheckr

Calculate strandness information of a bam file

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/strandCheckR.html
License:: GPL (>= 2)
Recipe:: /bioconductor-strandcheckr/meta.yaml

This package aims to quantify and remove putative double strand DNA from a strand-specific RNA sample. There are also options and methods to plot the positive/negative proportions of all sliding windows, which allow users to have an idea of how much the sample was contaminated and the appropriate threshold to be used for filtering.

package bioconductor-strandcheckr¶

Versions:

1.28.0-0, 1.24.0-0, 1.20.0-0, 1.18.0-0, 1.16.0-0, 1.12.0-0, 1.10.0-0, 1.8.0-1, 1.8.0-0,

1.28.0-0, 1.24.0-0, 1.20.0-0, 1.18.0-0, 1.16.0-0, 1.12.0-0, 1.10.0-0, 1.8.0-1, 1.8.0-0, 1.6.0-0, 1.4.0-0, 1.2.0-1, 1.0.0-0

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-genomicalignments >=1.46.0,<1.47.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-rsamtools >=2.26.0,<2.27.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.22.0,<3.23.0
on r-base >=4.5,<4.6.0a0
on r-dplyr
on r-ggplot2 >=4.0.0
on r-gridextra
on r-reshape2
on r-rlang
on r-stringr
on r-tidyselect

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-strandcheckr

to add into an existing workspace instead, run:

pixi add bioconductor-strandcheckr

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-strandcheckr

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-strandcheckr

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-strandcheckr:<tag>

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