Package Recipe 'bioconductor-timeomics'

recipe bioconductor-timeomics

Time-Course Multi-Omics data integration

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/timeOmics.html
License:: GPL-3
Recipe:: /bioconductor-timeomics/meta.yaml

timeOmics is a generic data-driven framework to integrate multi-Omics longitudinal data measured on the same biological samples and select key temporal features with strong associations within the same sample group. The main steps of timeOmics are: 1. Plaform and time-specific normalization and filtering steps; 2. Modelling each biological into one time expression profile; 3. Clustering features with the same expression profile over time; 4. Post-hoc validation step.

package bioconductor-timeomics¶

Versions:

1.22.0-0, 1.18.0-0, 1.14.0-0, 1.12.0-0, 1.10.0-0, 1.6.0-0, 1.4.0-0, 1.2.0-1, 1.2.0-0,

1.22.0-0, 1.18.0-0, 1.14.0-0, 1.12.0-0, 1.10.0-0, 1.6.0-0, 1.4.0-0, 1.2.0-1, 1.2.0-0, 1.0.0-0

Depends:

on bioconductor-mixomics >=6.34.0,<6.35.0
on r-base >=4.5,<4.6.0a0
on r-checkmate
on r-dplyr
on r-ggplot2
on r-ggrepel
on r-lmtest
on r-magrittr
on r-plyr
on r-purrr
on r-stringr
on r-tibble
on r-tidyr

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-timeomics

to add into an existing workspace instead, run:

pixi add bioconductor-timeomics

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-timeomics

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-timeomics

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-timeomics:<tag>

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