recipe bioconductor-guideseq

GUIDE-seq and PEtag-seq analysis pipeline

Homepage:

https://bioconductor.org/packages/3.18/bioc/html/GUIDEseq.html

License:

GPL (>= 2)

Recipe:

/bioconductor-guideseq/meta.yaml

Links:

biotools: guideseq, doi: 10.1186/s12864-017-3746-y

The package implements GUIDE-seq and PEtag-seq analysis workflow including functions for filtering UMI and reads with low coverage, obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites with mismatches and indels.

package bioconductor-guideseq

versions:

1.32.0-0,  1.30.0-0,  1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-0, 

1.32.0-0,  1.30.0-0,  1.28.0-0,  1.24.0-0,  1.22.0-0,  1.20.0-1,  1.20.0-0,  1.18.0-0,  1.16.0-0,  1.14.0-1,  1.12.0-0,  1.10.0-0,  1.8.0-0

depends bioconductor-biocgenerics:

>=0.48.0,<0.49.0

depends bioconductor-biostrings:

>=2.70.0,<2.71.0

depends bioconductor-bsgenome:

>=1.70.0,<1.71.0

depends bioconductor-chippeakanno:

>=3.36.0,<3.37.0

depends bioconductor-crisprseek:

>=1.42.0,<1.43.0

depends bioconductor-genomeinfodb:

>=1.38.0,<1.39.0

depends bioconductor-genomicalignments:

>=1.38.0,<1.39.0

depends bioconductor-genomicfeatures:

>=1.54.0,<1.55.0

depends bioconductor-genomicranges:

>=1.54.0,<1.55.0

depends bioconductor-iranges:

>=2.36.0,<2.37.0

depends bioconductor-limma:

>=3.58.0,<3.59.0

depends bioconductor-multtest:

>=2.58.0,<2.59.0

depends bioconductor-rsamtools:

>=2.18.0,<2.19.0

depends bioconductor-s4vectors:

>=0.40.0,<0.41.0

depends r-base:

>=4.3,<4.4.0a0

depends r-data.table:

depends r-dplyr:

depends r-ggplot2:

depends r-hash:

depends r-matrixstats:

depends r-openxlsx:

depends r-patchwork:

depends r-purrr:

depends r-rio:

depends r-rlang:

depends r-stringr:

depends r-tidyr:

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-guideseq

and update with::

   mamba update bioconductor-guideseq

To create a new environment, run:

mamba create --name myenvname bioconductor-guideseq

with myenvname being 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-guideseq:<tag>

(see `bioconductor-guideseq/tags`_ for valid values for ``<tag>``)

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