recipe bioconductor-txcutr

Transcriptome CUTteR

Homepage:

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

License:

GPL-3

Recipe:

/bioconductor-txcutr/meta.yaml

Various mRNA sequencing library preparation methods generate sequencing reads specifically from the transcript ends. Analyses that focus on quantification of isoform usage from such data can be aided by using truncated versions of transcriptome annotations, both at the alignment or pseudo-alignment stage, as well as in downstream analysis. This package implements some convenience methods for readily generating such truncated annotations and their corresponding sequences.

package bioconductor-txcutr

Versions:

1.4.0-0,  1.0.0-0

Depends:

• bioconductor-annotationdbi >=1.60.0,<1.61.0

• bioconductor-biocgenerics >=0.44.0,<0.45.0

• bioconductor-biocparallel >=1.32.0,<1.33.0

• bioconductor-biostrings >=2.66.0,<2.67.0

• 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-rtracklayer >=1.58.0,<1.59.0

• bioconductor-s4vectors >=0.36.0,<0.37.0

• r-base >=4.2,<4.3.0a0

Required By:

Installation

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

conda install bioconductor-txcutr

and update with:

conda update bioconductor-txcutr

or use the docker container:

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

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

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