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.
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crisprfunctionalgenomicsgenetargetbioconductorbioconductor-packagecrispr-cas9crispr-designcrispr-targetgenomics-analysisgrnagrna-sequencegrna-sequencessgrnasgrna-design
9.12 score 35 stars 3 dependents 126 scripts 525 downloadscrisprScore - 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, RuleSet3, DeepHF, 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 and enPAM+GB are not available on Windows machines.
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crisprfunctionalgenomicsfunctionalpredictionbioconductorbioconductor-packagecrispr-cas9crispr-designcrispr-targetgenomicsgrnagrna-sequencegrna-sequencesscoring-algorithmsgrnasgrna-design
8.16 score 31 stars 4 dependents 39 scripts 584 downloadscrisprBase - 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.
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crisprfunctionalgenomicsbioconductorbioconductor-packagecrispr-cas9crispr-designcrispr-targetgrnagrna-sequencegrna-sequences
7.36 score 6 stars 6 dependents 70 scripts 514 downloadsshinyMethyl - Interactive visualization for Illumina methylation arrays
Interactive tool for visualizing Illumina methylation array data. Both the 450k and EPIC array are supported.
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dnamethylationmicroarraytwochannelpreprocessingqualitycontrolmethylationarray
6.62 score 6 stars 682 downloadscrisprViz - 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.
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crisprfunctionalgenomicsgenetargetbioconductorbioconductor-packagecrispr-analysiscrispr-designgrnagrna-sequencegrna-sequencessgrnasgrna-designvisualization
5.98 score 8 stars 2 dependents 10 scripts 500 downloadscrisprBowtie - 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.
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crisprfunctionalgenomicsalignmentalignerbioconductorbioconductor-packagebowtiecrispr-analysiscrispr-cas9crispr-designcrispr-targetgrnagrna-sequencegrna-sequencessgrnasgrna-design
5.86 score 3 stars 4 dependents 10 scripts 490 downloadscrisprScoreData - Pre-trained models for the crisprScore package
Provides an interface to access pre-trained models for on-target and off-target gRNA activity prediction algorithms implemented in the crisprScore package. Pre-trained model data are stored in the ExperimentHub database. Users should consider using the crisprScore package directly to use and load the pre-trained models.
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experimenthubhomo_sapiens_databioconductorbioconductor-packagecrisprcrispr-analysiscrispr-cas9crispr-designcrispr-targetgrnagrna-sequencegrna-sequencesscoring-modelssgrnasgrna-designdatapkg
5.78 score 2 stars 5 dependents 4 scriptscrisprVerse - 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>.
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crisprfunctionalgenomicsgenetargetcrispr-analysiscrispr-designcrispr-targetgrnagrna-sequencegrna-sequences
5.18 score 15 stars 10 scripts 357 downloadscrisprBwa - 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.
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crisprfunctionalgenomicsalignmentalignerbioconductorbioconductor-packagebwacrispr-analysiscrispr-cas9crispr-designcrispr-targetgrnagrna-sequencegrna-sequencessgrnasgrna-design
4.95 score 2 stars 10 scripts 347 downloadscrisprShiny - 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.
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crisprfunctionalgenomicsgenetargetguicrispr-analysiscrispr-designshiny
4.89 score 2 stars 13 scripts 330 downloadsRbwa - 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.
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sequencingalignmentbwabwa-memdna-sequencesdna-sequencing
4.88 score 1 stars 1 dependents 21 scripts 313 downloads