recipe bioconductor-tximeta

Transcript Quantification Import with Automatic Metadata

Homepage:

https://bioconductor.org/packages/3.16/bioc/html/tximeta.html

License:

GPL-2

Recipe:

/bioconductor-tximeta/meta.yaml

Transcript quantification import from Salmon and alevin with automatic attachment of transcript ranges and release information, and other associated metadata. De novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for computational reproducibility.

package bioconductor-tximeta

Versions:

1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.4-0,  1.8.0-0,  1.6.3-0,  1.6.2-0,  1.4.3-0, 

1.16.0-0,  1.14.0-0,  1.12.0-0,  1.10.0-0,  1.8.4-0,  1.8.0-0,  1.6.3-0,  1.6.2-0,  1.4.3-0,  1.4.0-0,  1.2.2-0,  1.0.3-0,  1.0.1-0

Depends:

• bioconductor-annotationdbi >=1.60.0,<1.61.0

• bioconductor-annotationhub >=3.6.0,<3.7.0

• bioconductor-biocfilecache >=2.6.0,<2.7.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• bioconductor-ensembldb >=2.22.0,<2.23.0

• bioconductor-genomeinfodb >=1.34.0,<1.35.0

• bioconductor-genomicfeatures >=1.50.0,<1.51.0

• bioconductor-genomicranges >=1.50.0,<1.51.0

• bioconductor-iranges >=2.32.0,<2.33.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• bioconductor-summarizedexperiment >=1.28.0,<1.29.0

• bioconductor-tximport >=1.26.0,<1.27.0

• r-base >=4.2,<4.3.0a0

• r-jsonlite

• r-matrix

• r-tibble

Required By:

• bioconductor-isoformswitchanalyzer

Installation

With an activated Bioconda channel (see set-up-channels), install with:

conda install bioconductor-tximeta

and update with:

conda update bioconductor-tximeta

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-tximeta:<tag>

(see bioconductor-tximeta/tags for valid values for <tag>)

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