crisprDesign - Comprehensive design of CRISPR gRNAs for nucleases and base editors

Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. This includes on- and off-target search, on-target efficiency scoring, off-target scoring, full gene and TSS contextual annotations, and SNP annotation (human only). It currently support five types of CRISPR modalities (modes of perturbations): CRISPR knockout, CRISPR activation, CRISPR inhibition, CRISPR base editing, and CRISPR knockdown. All types of CRISPR nucleases are supported, including DNA- and RNA-target nucleases such as Cas9, Cas12a, and Cas13d. All types of base editors are also supported. gRNA design can be performed on reference genomes, transcriptomes, and custom DNA and RNA sequences. Both unpaired and paired gRNA designs are enabled.

Last updated 24 days ago

crisprfunctionalgenomicsgenetargetbioconductorbioconductor-packagecrispr-cas9crispr-designcrispr-targetgenomics-analysisgrnagrna-sequencegrna-sequencessgrnasgrna-design

8.20 score 19 stars 3 packages 78 scripts 286 downloads

crisprScore - On-Target and Off-Target Scoring Algorithms for CRISPR gRNAs

Provides R wrappers of several on-target and off-target scoring methods for CRISPR guide RNAs (gRNAs). The following nucleases are supported: SpCas9, AsCas12a, enAsCas12a, and RfxCas13d (CasRx). The available on-target cutting efficiency scoring methods are RuleSet1, Azimuth, DeepHF, DeepCpf1, enPAM+GB, and CRISPRscan. Both the CFD and MIT scoring methods are available for off-target specificity prediction. The package also provides a Lindel-derived score to predict the probability of a gRNA to produce indels inducing a frameshift for the Cas9 nuclease. Note that DeepHF, DeepCpf1 and enPAM+GB are not available on Windows machines.

Last updated 24 days ago

crisprfunctionalgenomicsfunctionalpredictionbioconductorbioconductor-packagecrispr-cas9crispr-designcrispr-targetgenomicsgrnagrna-sequencegrna-sequencesscoring-algorithmsgrnasgrna-design

7.44 score 13 stars 4 packages 17 scripts 311 downloads

shinyMethyl - Interactive visualization for Illumina methylation arrays

Interactive tool for visualizing Illumina methylation array data. Both the 450k and EPIC array are supported.

Last updated 24 days ago

dnamethylationmicroarraytwochannelpreprocessingqualitycontrolmethylationarray

7.42 score 5 stars 38 scripts 422 downloads

crisprBase - Base functions and classes for CRISPR gRNA design

Provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors.Several CRISPR-specific genome arithmetic functions are implemented to help extract genomic coordinates of spacer and protospacer sequences. Commonly-used CRISPR nuclease objects are provided that can be readily used in other packages. Both DNA- and RNA-targeting nucleases are supported.

Last updated 24 days ago

crisprfunctionalgenomicsbioconductorbioconductor-packagecrispr-cas9crispr-designcrispr-targetgrnagrna-sequencegrna-sequences

7.18 score 4 stars 6 packages 52 scripts 298 downloads

crisprViz - Visualization Functions for CRISPR gRNAs

Provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on genomic tracks across nucleases and applications. Works in conjunction with the crisprBase and crisprDesign Bioconductor packages. Plots are produced using the Gviz framework.

Last updated 24 days ago

crisprfunctionalgenomicsgenetargetbioconductorbioconductor-packagecrispr-analysiscrispr-designgrnagrna-sequencegrna-sequencessgrnasgrna-designvisualization

6.08 score 5 stars 2 packages 6 scripts 190 downloads

crisprBowtie - Bowtie-based alignment of CRISPR gRNA spacer sequences

Provides a user-friendly interface to map on-targets and off-targets of CRISPR gRNA spacer sequences using bowtie. The alignment is fast, and can be performed using either commonly-used or custom CRISPR nucleases. The alignment can work with any reference or custom genomes. Both DNA- and RNA-targeting nucleases are supported.

Last updated 24 days ago

crisprfunctionalgenomicsalignmentalignerbioconductorbioconductor-packagebowtiecrispr-analysiscrispr-cas9crispr-designcrispr-targetgrnagrna-sequencegrna-sequencessgrnasgrna-design

5.68 score 2 stars 4 packages 7 scripts 285 downloads

crisprVerse - Easily install and load the crisprVerse ecosystem for CRISPR gRNA design

The crisprVerse is a modular ecosystem of R packages developed for the design and manipulation of CRISPR guide RNAs (gRNAs). All packages share a common language and design principles. This package is designed to make it easy to install and load the crisprVerse packages in a single step. To learn more about the crisprVerse, visit <https://www.github.com/crisprVerse>.

Last updated 24 days ago

crisprfunctionalgenomicsgenetargetcrispr-analysiscrispr-designcrispr-targetgrnagrna-sequencegrna-sequences

5.08 score 12 stars 8 scripts 226 downloads

crisprShiny - Exploring curated CRISPR gRNAs via Shiny

Provides means to interactively visualize guide RNAs (gRNAs) in GuideSet objects via Shiny application. This GUI can be self-contained or as a module within a larger Shiny app. The content of the app reflects the annotations present in the passed GuideSet object, and includes intuitive tools to examine, filter, and export gRNAs, thereby making gRNA design more user-friendly.

Last updated 24 days ago

crisprfunctionalgenomicsgenetargetguicrispr-analysiscrispr-designshiny

4.85 score 2 stars 8 scripts 140 downloads

crisprBwa - BWA-based alignment of CRISPR gRNA spacer sequences

Provides a user-friendly interface to map on-targets and off-targets of CRISPR gRNA spacer sequences using bwa. The alignment is fast, and can be performed using either commonly-used or custom CRISPR nucleases. The alignment can work with any reference or custom genomes. Currently not supported on Windows machines.

Last updated 24 days ago

crisprfunctionalgenomicsalignmentalignerbioconductorbioconductor-packagebwacrispr-analysiscrispr-cas9crispr-designcrispr-targetgrnagrna-sequencegrna-sequencessgrnasgrna-design

4.30 score 1 stars 6 scripts 162 downloads

Rbwa - R wrapper for BWA-backtrack and BWA-MEM aligners

Provides an R wrapper for BWA alignment algorithms. Both BWA-backtrack and BWA-MEM are available. Convenience function to build a BWA index from a reference genome is also provided. Currently not supported for Windows machines.

Last updated 24 days ago

sequencingalignmentbwabwa-memdna-sequencesdna-sequencing

4.26 score 1 packages 10 scripts 154 downloads