Package Recipe 'bioconductor-guideseq'

recipe bioconductor-guideseq

GUIDE-seq and PEtag-seq analysis pipeline

Homepage:: https://bioconductor.org/packages/3.20/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:

1.40.0-0, 1.36.0-0, 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,

1.40.0-0, 1.36.0-0, 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:

on bioconductor-biocgenerics >=0.56.0,<0.57.0
on bioconductor-biostrings >=2.78.0,<2.79.0
on bioconductor-bsgenome >=1.78.0,<1.79.0
on bioconductor-chippeakanno >=3.44.0,<3.45.0
on bioconductor-crisprseek >=1.50.0,<1.51.0
on bioconductor-genomeinfodb >=1.46.0,<1.47.0
on bioconductor-genomicalignments >=1.46.0,<1.47.0
on bioconductor-genomicfeatures >=1.62.0,<1.63.0
on bioconductor-genomicranges >=1.62.0,<1.63.0
on bioconductor-iranges >=2.44.0,<2.45.0
on bioconductor-limma >=3.66.0,<3.67.0
on bioconductor-multtest >=2.66.0,<2.67.0
on bioconductor-pwalign >=1.6.0,<1.7.0
on bioconductor-rsamtools >=2.26.0,<2.27.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-dplyr
on r-ggplot2
on r-hash
on r-matrixstats
on r-openxlsx
on r-patchwork
on r-purrr
on r-rio
on r-rlang
on r-stringr
on r-tidyr

Additional platforms:

Installation¶

You need a conda-compatible package manager (currently either pixi, conda, or micromamba) and the Bioconda channel already activated (see Usage). Below, we show how to install with either pixi or conda (for micromamba and mamba, commands are essentially the same as with conda).

Pixi¶

With pixi installed and the Bioconda channel set up (see Usage), to install globally, run:

pixi global install bioconductor-guideseq

to add into an existing workspace instead, run:

pixi add bioconductor-guideseq

In the latter case, make sure to first add bioconda and conda-forge to the channels considered by the workspace:

pixi workspace channel add conda-forge
pixi workspace channel add bioconda

Conda¶

With conda installed and the Bioconda channel set up (see Usage), to install into an existing and activated environment, run:

conda install bioconductor-guideseq

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-guideseq

with envname being the name of the desired environment.

Container¶

Alternatively, every Bioconda package is available as a container image for usage with your preferred container runtime. For e.g. docker, run:

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

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

Integrated deployment¶

Finally, note that many scientific workflow management systems directly integrate both conda and container based software deployment. Thus, workflow steps can be often directly annotated to use the package, leading to automatic deployment by the respective workflow management system, thereby improving reproducibility and transparency. Check the documentation of your workflow management system to find out about the integration.

Download stats¶

Link to this page¶

Render an badge with the following MarkDown:

[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-guideseq/README.html)