Package Recipe 'bioconductor-isoformswitchanalyzer'

recipe bioconductor-isoformswitchanalyzer

Identify, Annotate and Visualize Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/IsoformSwitchAnalyzeR.html
License:: GPL (>= 2)
Recipe:: /bioconductor-isoformswitchanalyzer/meta.yaml
Links:: biotools: IsoformSwitchAnalyzeR, doi: 10.1158/1541-7786.MCR-16-0459

Analysis of alternative splicing and isoform switches with predicted functional consequences (e.g. gain/loss of protein domains etc.) from quantification of all types of RNASeq by tools such as Kallisto, Salmon, StringTie, Cufflinks/Cuffdiff etc.

package bioconductor-isoformswitchanalyzer¶

Versions:

2.10.0-0, 2.6.0-0, 2.2.0-0, 2.0.1-0, 1.20.0-1, 1.20.0-0, 1.16.0-2, 1.16.0-1, 1.16.0-0,

2.10.0-0, 2.6.0-0, 2.2.0-0, 2.0.1-0, 1.20.0-1, 1.20.0-0, 1.16.0-2, 1.16.0-1, 1.16.0-0, 1.14.0-0, 1.12.0-1, 1.12.0-0, 1.10.0-0, 1.8.0-0, 1.6.0-1, 1.4.0-0, 1.2.0-0, 1.0.0-0

Depends:

on bioconductor-biobase >=2.70.0,<2.71.0
on bioconductor-biobase >=2.70.0,<2.71.0a0
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-dexseq >=1.56.0,<1.57.0
on bioconductor-dexseq >=1.56.0,<1.57.0a0
on bioconductor-edger >=4.8.0,<4.9.0
on bioconductor-edger >=4.8.2,<4.9.0a0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.1,<1.63.0a0
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-pfamanalyzer >=1.10.0,<1.11.0
on bioconductor-pfamanalyzer >=1.10.0,<1.11.0a0
on bioconductor-pwalign >=1.6.0,<1.7.0
on bioconductor-pwalign >=1.6.0,<1.7.0a0
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-saturn >=1.18.0,<1.19.0
on bioconductor-saturn >=1.18.0,<1.19.0a0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on bioconductor-seqinfo >=1.0.0,<1.1.0a0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0
on bioconductor-summarizedexperiment >=1.40.0,<1.41.0a0
on bioconductor-sva >=3.58.0,<3.59.0
on bioconductor-sva >=3.58.0,<3.59.0a0
on bioconductor-tximeta >=1.28.0,<1.29.0
on bioconductor-tximeta >=1.28.2,<1.29.0a0
on bioconductor-tximport >=1.38.0,<1.39.0
on bioconductor-tximport >=1.38.2,<1.39.0a0
on bioconductor-xvector >=0.50.0,<0.51.0
on bioconductor-xvector >=0.50.0,<0.51.0a0
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-dbi
on r-dplyr
on r-futile.logger
on r-ggplot2 >=3.3.5
on r-gridextra
on r-magrittr
on r-plyr
on r-rcolorbrewer
on r-rcurl
on r-readr
on r-reshape2
on r-stringr
on r-tibble
on r-tidyr
on r-venndiagram

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-isoformswitchanalyzer

to add into an existing workspace instead, run:

pixi add bioconductor-isoformswitchanalyzer

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-isoformswitchanalyzer

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-isoformswitchanalyzer

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-isoformswitchanalyzer:<tag>

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