- 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/3.18/bioc/html/IsoformSwitchAnalyzeR.html
- License:
GPL (>= 2)
- Recipe:
- 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:
2.2.0-0,2.0.1-0,1.20.0-1,1.20.0-0,1.16.0-2,1.16.0-1,1.16.0-0,1.14.0-0,1.12.0-1,2.2.0-0,2.0.1-0,1.20.0-1,1.20.0-0,1.16.0-2,1.16.0-1,1.16.0-0,1.14.0-0,1.12.0-1,1.12.0-0,1.10.0-0,1.8.0-0,1.6.0-1,1.4.0-0,1.2.0-0,1.0.0-0- depends bioconductor-biobase:
>=2.62.0,<2.63.0- depends bioconductor-biobase:
>=2.62.0,<2.63.0a0- depends bioconductor-biocgenerics:
>=0.48.0,<0.49.0- depends bioconductor-biocgenerics:
>=0.48.1,<0.49.0a0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0- depends bioconductor-biocparallel:
>=1.36.0,<1.37.0a0- depends bioconductor-biostrings:
>=2.70.0,<2.71.0- depends bioconductor-biostrings:
>=2.70.1,<2.71.0a0- depends bioconductor-bsgenome:
>=1.70.0,<1.71.0- depends bioconductor-bsgenome:
>=1.70.1,<1.71.0a0- depends bioconductor-dexseq:
>=1.48.0,<1.49.0- depends bioconductor-dexseq:
>=1.48.0,<1.49.0a0- depends bioconductor-edger:
>=4.0.0,<4.1.0- depends bioconductor-edger:
>=4.0.2,<4.1.0a0- depends bioconductor-genomeinfodb:
>=1.38.0,<1.39.0- depends bioconductor-genomeinfodb:
>=1.38.1,<1.39.0a0- depends bioconductor-genomicranges:
>=1.54.0,<1.55.0- depends bioconductor-genomicranges:
>=1.54.1,<1.55.0a0- depends bioconductor-iranges:
>=2.36.0,<2.37.0- depends bioconductor-iranges:
>=2.36.0,<2.37.0a0- depends bioconductor-limma:
>=3.58.0,<3.59.0- depends bioconductor-limma:
>=3.58.1,<3.59.0a0- depends bioconductor-pfamanalyzer:
>=1.2.0,<1.3.0- depends bioconductor-pfamanalyzer:
>=1.2.0,<1.3.0a0- depends bioconductor-rtracklayer:
>=1.62.0,<1.63.0- depends bioconductor-rtracklayer:
>=1.62.0,<1.63.0a0- depends bioconductor-s4vectors:
>=0.40.0,<0.41.0- depends bioconductor-s4vectors:
>=0.40.2,<0.41.0a0- depends bioconductor-saturn:
>=1.10.0,<1.11.0- depends bioconductor-saturn:
>=1.10.0,<1.11.0a0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0- depends bioconductor-summarizedexperiment:
>=1.32.0,<1.33.0a0- depends bioconductor-sva:
>=3.50.0,<3.51.0- depends bioconductor-sva:
>=3.50.0,<3.51.0a0- depends bioconductor-tximeta:
>=1.20.0,<1.21.0- depends bioconductor-tximeta:
>=1.20.1,<1.21.0a0- depends bioconductor-tximport:
>=1.30.0,<1.31.0- depends bioconductor-tximport:
>=1.30.0,<1.31.0a0- depends bioconductor-xvector:
>=0.42.0,<0.43.0- depends bioconductor-xvector:
>=0.42.0,<0.43.0a0- depends libblas:
>=3.9.0,<4.0a0- depends libgcc-ng:
>=12- depends liblapack:
>=3.9.0,<4.0a0- depends r-base:
>=4.3,<4.4.0a0- depends r-dbi:
- depends r-dplyr:
- depends r-futile.logger:
- depends r-ggplot2:
>=3.3.5- 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:
- 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-isoformswitchanalyzer and update with:: mamba update bioconductor-isoformswitchanalyzer
To create a new environment, run:
mamba create --name myenvname bioconductor-isoformswitchanalyzer
with
myenvnamebeing 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-isoformswitchanalyzer:<tag> (see `bioconductor-isoformswitchanalyzer/tags`_ for valid values for ``<tag>``)
Download stats¶
Link to this page¶
Render an 
badge with the following MarkDown:
[](http://bioconda.github.io/recipes/bioconductor-isoformswitchanalyzer/README.html)
