Package Recipe 'bioconductor-qsea'

recipe bioconductor-qsea

IP-seq data analysis and vizualization

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/qsea.html
License:: GPL-2
Recipe:: /bioconductor-qsea/meta.yaml
Links:: biotools: qsea

qsea (quantitative sequencing enrichment analysis) was developed as the successor of the MEDIPS package for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, qsea provides several functionalities for the analysis of other kinds of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential enrichment between groups of samples.

package bioconductor-qsea¶

Versions:

1.36.0-0, 1.32.0-0, 1.28.0-0, 1.26.0-0, 1.24.0-1, 1.24.0-0, 1.20.0-2, 1.20.0-1, 1.20.0-0,

1.36.0-0, 1.32.0-0, 1.28.0-0, 1.26.0-0, 1.24.0-1, 1.24.0-0, 1.20.0-2, 1.20.0-1, 1.20.0-0, 1.18.0-0, 1.16.0-1, 1.16.0-0, 1.14.0-0, 1.12.0-0, 1.10.0-1, 1.8.0-0, 1.6.0-0, 1.4.0-0

Depends:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biocgenerics >=0.56.0,<0.57.0a0
on bioconductor-biocparallel >=1.44.0,<1.45.0
on bioconductor-biocparallel >=1.44.0,<1.45.0a0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-biostrings >=2.78.0,<2.79.0a0
on bioconductor-bsgenome >=1.78.0,<1.79.0
on bioconductor-bsgenome >=1.78.0,<1.79.0a0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.1,<1.63.0a0
on bioconductor-hmmcopy >=1.52.0,<1.53.0
on bioconductor-hmmcopy >=1.52.0,<1.53.0a0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-iranges >=2.44.0,<2.45.0a0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-limma >=3.66.0,<3.67.0a0
on bioconductor-rsamtools >=2.26.0,<2.27.0
on bioconductor-rsamtools >=2.26.0,<2.27.0a0
on bioconductor-rtracklayer >=1.70.0,<1.71.0
on bioconductor-rtracklayer >=1.70.1,<1.71.0a0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-s4vectors >=0.48.0,<0.49.0a0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on bioconductor-seqinfo >=1.0.0,<1.1.0a0
on libblas >=3.9.0,<4.0a0
on libgcc >=14
on liblapack >=3.9.0,<4.0a0
on liblzma >=5.8.2,<6.0a0
on libzlib >=1.3.1,<2.0a0
on r-base >=4.5,<4.6.0a0
on r-gtools
on r-zoo

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-qsea

to add into an existing workspace instead, run:

pixi add bioconductor-qsea

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-qsea

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-qsea

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-qsea:<tag>

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