Package Recipe 'bioconductor-seqarchr'

recipe bioconductor-seqarchr

Identify Different Architectures of Sequence Elements

Homepage:: https://bioconductor.org/packages/3.18/bioc/html/seqArchR.html
License:: GPL-3 | file LICENSE
Recipe:: /bioconductor-seqarchr/meta.yaml

seqArchR enables unsupervised discovery of _de novo_ clusters with characteristic sequence architectures characterized by position-specific motifs or composition of stretches of nucleotides, e.g., CG-richness. seqArchR does _not_ require any specifications w.r.t. the number of clusters, the length of any individual motifs, or the distance between motifs if and when they occur in pairs/groups; it directly detects them from the data. seqArchR uses non-negative matrix factorization (NMF) as its backbone, and employs a chunking-based iterative procedure that enables processing of large sequence collections efficiently. Wrapper functions are provided for visualizing cluster architectures as sequence logos.

package bioconductor-seqarchr¶

Versions:

1.6.0-0, 1.4.0-0, 1.2.0-0

Depends:

on bioconductor-biocparallel >=1.36.0,<1.37.0
on bioconductor-biostrings >=2.70.0,<2.71.0
on r-base >=4.3,<4.4.0a0
on r-cli
on r-cluster
on r-cvtools >=0.3.2
on r-fpc
on r-ggplot2 >=3.1.1
on r-ggseqlogo >=0.1
on r-mass
on r-matrix
on r-matrixstats
on r-prettyunits
on r-reshape2 >=1.4.3
on r-reticulate >=1.22

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-seqarchr

to add into an existing workspace instead, run:

pixi add bioconductor-seqarchr

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-seqarchr

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-seqarchr

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-seqarchr:<tag>

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