- recipe bioconductor-isoformswitchanalyzer
Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read RNA-seq data.
- Homepage
https://bioconductor.org/packages/3.14/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
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
,1.16.0-1
,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
>=2.54.0,<2.55.0
bioconductor-biocgenerics
>=0.40.0,<0.41.0
bioconductor-biostrings
>=2.62.0,<2.63.0
bioconductor-bsgenome
>=1.62.0,<1.63.0
bioconductor-dexseq
>=1.40.0,<1.41.0
bioconductor-drimseq
>=1.22.0,<1.23.0
bioconductor-edger
>=3.36.0,<3.37.0
bioconductor-genomeinfodb
>=1.30.0,<1.31.0
bioconductor-genomicranges
>=1.46.0,<1.47.0
bioconductor-iranges
>=2.28.0,<2.29.0
bioconductor-limma
>=3.50.0,<3.51.0
bioconductor-rtracklayer
>=1.54.0,<1.55.0
bioconductor-tximeta
>=1.12.0,<1.13.0
bioconductor-tximport
>=1.22.0,<1.23.0
bioconductor-xvector
>=0.34.0,<0.35.0
libblas
>=3.8.0,<4.0a0
libgcc-ng
>=10.3.0
liblapack
>=3.8.0,<4.0a0
r-base
>=4.1,<4.2.0a0
- Required By
Installation
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install bioconductor-isoformswitchanalyzer
and update with:
conda update bioconductor-isoformswitchanalyzer
or 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)