recipe bioconductor-surfaltr

Rapid Comparison of Surface Protein Isoform Membrane Topologies Through surfaltr

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/surfaltr.html

License:

MIT + file LICENSE

Recipe:

/bioconductor-surfaltr/meta.yaml

Cell surface proteins form a major fraction of the druggable proteome and can be used for tissue-specific delivery of oligonucleotide/cell-based therapeutics. Alternatively spliced surface protein isoforms have been shown to differ in their subcellular localization and/or their transmembrane (TM) topology. Surface proteins are hydrophobic and remain difficult to study thereby necessitating the use of TM topology prediction methods such as TMHMM and Phobius. However, there exists a need for bioinformatic approaches to streamline batch processing of isoforms for comparing and visualizing topologies. To address this gap, we have developed an R package, surfaltr. It pairs inputted isoforms, either known alternatively spliced or novel, with their APPRIS annotated principal counterparts, predicts their TM topologies using TMHMM or Phobius, and generates a customizable graphical output. Further, surfaltr facilitates the prioritization of biologically diverse isoform pairs through the incorporation of three different ranking metrics and through protein alignment functions. Citations for programs mentioned here can be found in the vignette.

package bioconductor-surfaltr

versions:

1.8.0-0,  1.6.0-0,  1.4.0-0,  1.0.0-0

depends bioconductor-biomart:

>=2.58.0,<2.59.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-msa:

>=1.34.0,<1.35.0

depends r-base:

>=4.3,<4.4.0a0

depends r-dplyr:

>=1.0.6

depends r-ggplot2:

>=3.3.2

depends r-httr:

>=1.4.2

depends r-protr:

>=1.6-2

depends r-readr:

>=1.4.0

depends r-seqinr:

>=4.2-5

depends r-stringr:

>=1.4.0

depends r-testthat:

>=3.0.0

depends r-xml2:

>=1.3.2

requirements:

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-surfaltr

and update with::

   mamba update bioconductor-surfaltr

To create a new environment, run:

mamba create --name myenvname bioconductor-surfaltr

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-surfaltr:<tag>

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

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