recipe bioconductor-seahtrue

Seahtrue revives XF data for structured data analysis

Homepage:

https://bioconductor.org/packages/3.20/bioc/html/seahtrue.html

License:

Artistic-2.0

Recipe:

/bioconductor-seahtrue/meta.yaml

Seahtrue organizes oxygen consumption and extracellular acidification analysis data from experiments performed on an XF analyzer into structured nested tibbles.This allows for detailed processing of raw data and advanced data visualization and statistics. Seahtrue introduces an open and reproducible way to analyze these XF experiments. It uses file paths to .xlsx files. These .xlsx files are supplied by the userand are generated by the user in the Wave software from Agilent from the assay result files (.asyr). The .xlsx file contains different sheets of important data for the experiment; 1. Assay Information - Details about how the experiment was set up. 2. Rate Data - Information about the OCR and ECAR rates. 3. Raw Data - The original raw data collected during the experiment. 4. Calibration Data - Data related to calibrating the instrument. Seahtrue focuses on getting the specific data needed for analysis. Once this data is extracted, it is prepared for calculations through preprocessing. To make sure everything is accurate, both the initial data and the preprocessed data go through thorough checks.

package bioconductor-seahtrue

versions:

1.0.0-0

depends r-base:

>=4.4,<4.5.0a0

depends r-cli:

>=3.4.1

depends r-colorspace:

>=2.1.0

depends r-dplyr:

>=1.1.2

depends r-forcats:

>=1.0.0

depends r-ggplot2:

>=3.5.0

depends r-ggridges:

>=0.5.6

depends r-glue:

>=1.6.2

depends r-janitor:

>=2.2.0

depends r-logger:

>=0.2.2

depends r-lubridate:

>=1.8.0

depends r-purrr:

>=0.3.5

depends r-rcolorbrewer:

>=1.1.3

depends r-readr:

>=2.1.5

depends r-readxl:

>=1.4.1

depends r-rlang:

>=1.0.0

depends r-scales:

>=1.3.0

depends r-stringr:

>=1.4.1

depends r-tibble:

>=3.1.8

depends r-tidyr:

>=1.3.0

depends r-tidyxl:

>=1.0.8

depends r-validate:

>=1.1.1

requirements:

additional platforms:

Installation

You need a conda-compatible package manager (currently either micromamba, mamba, or conda) and the Bioconda channel already activated (see set-up-channels).

While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see here for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others.

Given that you already have a conda environment in which you want to have this package, install with:

   mamba install bioconductor-seahtrue

and update with::

   mamba update bioconductor-seahtrue

To create a new environment, run:

mamba create --name myenvname bioconductor-seahtrue

with myenvname being a reasonable name for the environment (see e.g. the mamba docs for details and further options).

Alternatively, use the docker container:

   docker pull quay.io/biocontainers/bioconductor-seahtrue:<tag>

(see `bioconductor-seahtrue/tags`_ for valid values for ``<tag>``)

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