- 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/3.16/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:
1.20.0-1
,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
,1.20.0-1
,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
>=2.58.0,<2.59.0
bioconductor-biocgenerics
>=0.44.0,<0.45.0
bioconductor-biostrings
>=2.66.0,<2.67.0
bioconductor-bsgenome
>=1.66.0,<1.67.0
bioconductor-dexseq
>=1.44.0,<1.45.0
bioconductor-drimseq
>=1.26.0,<1.27.0
bioconductor-edger
>=3.40.0,<3.41.0
bioconductor-genomeinfodb
>=1.34.0,<1.35.0
bioconductor-genomicranges
>=1.50.0,<1.51.0
bioconductor-iranges
>=2.32.0,<2.33.0
bioconductor-limma
>=3.54.0,<3.55.0
bioconductor-rtracklayer
>=1.58.0,<1.59.0
bioconductor-tximeta
>=1.16.0,<1.17.0
bioconductor-tximport
>=1.26.0,<1.27.0
bioconductor-xvector
>=0.38.0,<0.39.0
libblas
>=3.9.0,<4.0a0
libgcc-ng
>=12
liblapack
>=3.9.0,<4.0a0
r-base
>=4.2,<4.3.0a0
- Required By:
Installation
With an activated Bioconda channel (see 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)