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 2 months ago

dnamethylationmicroarraytwochannelpreprocessingqualitycontrolmethylationarray

3.31 score 148 dependencies

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 1 months ago

crisprfunctionalgenomicsfunctionalprediction

13 stars 2.42 score 72 dependencies 4 dependents

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 2 months ago

crisprfunctionalgenomics

4 stars 2.14 score 27 dependencies 6 dependents

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 2 months ago

crisprfunctionalgenomicsgenetarget

1.69 score 117 dependencies 3 dependents

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 4 months ago

crisprfunctionalgenomicsalignment

2 stars 1.64 score 76 dependencies 4 dependents

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 4 months ago

crisprfunctionalgenomicsgenetarget

5 stars 1.58 score 170 dependencies 2 dependents

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 4 months ago

crisprfunctionalgenomicsgenetarget

11 stars 1.38 score 171 dependencies

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 4 months ago

crisprfunctionalgenomicsgenetargetgui

2 stars 0.91 score 184 dependencies

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 4 months ago

sequencingalignment

0.91 score 0 dependencies 1 dependents

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 4 months ago

crisprfunctionalgenomicsalignment

1 stars 0.61 score 76 dependencies