Package Recipe 'bioconductor-crisprseek'

recipe bioconductor-crisprseek

Design of target-specific guide RNAs in CRISPR-Cas9, genome-editing systems

Homepage:: https://bioconductor.org/packages/3.20/bioc/html/CRISPRseek.html
License:: GPL (>= 2)
Recipe:: /bioconductor-crisprseek/meta.yaml
Links:: biotools: crisprseek

The package includes functions to find potential guide RNAs for the CRISPR editing system including Base Editors and the Prime Editor for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not. Potential guide RNAs are annotated with total score of the top5 and topN off-targets, detailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs. The package also output 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)