recipe bioconductor-isoformswitchanalyzer

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



GPL (>= 2)




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

(downloads) docker_bioconductor-isoformswitchanalyzer



depends bioconductor-biobase:


depends bioconductor-biocgenerics:


depends bioconductor-biocparallel:


depends bioconductor-biostrings:


depends bioconductor-bsgenome:


depends bioconductor-dexseq:


depends bioconductor-edger:


depends bioconductor-genomeinfodb:


depends bioconductor-genomicranges:


depends bioconductor-iranges:


depends bioconductor-limma:


depends bioconductor-pfamanalyzer:


depends bioconductor-rtracklayer:


depends bioconductor-s4vectors:


depends bioconductor-saturn:


depends bioconductor-summarizedexperiment:


depends bioconductor-sva:


depends bioconductor-tximeta:


depends bioconductor-tximport:


depends bioconductor-xvector:


depends libblas:


depends libgcc-ng:


depends liblapack:


depends r-base:


depends r-dbi:

depends r-dplyr:

depends r-futile.logger:

depends r-ggplot2:


depends r-gridextra:

depends r-magrittr:

depends r-plyr:

depends r-rcolorbrewer:

depends r-rcurl:

depends r-readr:

depends r-reshape2:

depends r-stringr:

depends r-tibble:

depends r-tidyr:

depends r-venndiagram:



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-isoformswitchanalyzer

and update with::

   mamba update bioconductor-isoformswitchanalyzer

To create a new environment, run:

mamba create --name myenvname bioconductor-isoformswitchanalyzer

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<tag>

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

Download stats