Package Recipe 'bioconductor-crisprseek'

recipe bioconductor-crisprseek

Design of guide RNAs in CRISPR genome-editing systems

Homepage:: https://bioconductor.org/packages/3.22/bioc/html/CRISPRseek.html
License:: file LICENSE
Recipe:: /bioconductor-crisprseek/meta.yaml
Links:: biotools: crisprseek

The package encompasses functions to find potential guide RNAs for the CRISPR-based genome-editing systems including the Base Editors and the Prime Editors when supplied with target sequences as input. Users have the flexibility to filter resulting guide RNAs based on parameters such as the absence of restriction enzyme cut sites or the lack of paired guide RNAs. The package also facilitates genome-wide exploration for off-targets, offering features to score and rank off-targets, retrieve flanking sequences, and indicate whether the hits are located within exon regions. All detected guide RNAs are annotated with the cumulative scores of the top5 and topN off-targets together with the detailed information such as mismatch sites and restrictuion enzyme cut sites. The package also outputs INDELs and their frequencies for Cas9 targeted sites.

package bioconductor-crisprseek¶

Versions:

1.50.0-0, 1.46.0-0, 1.42.0-0, 1.40.0-0, 1.38.0-0, 1.34.0-0, 1.32.0-0, 1.30.1-0, 1.30.0-0,

1.50.0-0, 1.46.0-0, 1.42.0-0, 1.40.0-0, 1.38.0-0, 1.34.0-0, 1.32.0-0, 1.30.1-0, 1.30.0-0, 1.28.0-0, 1.26.0-0, 1.24.0-1, 1.22.0-0, 1.20.0-0, 1.18.0-0

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-delayedarray >=0.36.0,<0.37.0
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-rhdf5 >=2.54.0,<2.55.0
on bioconductor-s4vectors >=0.48.0,<0.49.0
on bioconductor-seqinfo >=1.0.0,<1.1.0
on bioconductor-xvector >=0.50.0,<0.51.0
on r-base >=4.5,<4.6.0a0
on r-data.table
on r-dplyr
on r-gtools
on r-hash
on r-keras
on r-mltools
on r-openxlsx
on r-reticulate
on r-rio
on r-rlang
on r-seqinr
on r-stringr

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-crisprseek

to add into an existing workspace instead, run:

pixi add bioconductor-crisprseek

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-crisprseek

Alternatively, to install into a new environment, run:

conda create -n envname bioconductor-crisprseek

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-crisprseek:<tag>

(see bioconductor-crisprseek/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-crisprseek/README.html)