Overview | Installation and getting started | Software requirements | OS Requirements | Installation from Bioconductor | Installation from GitHub | Python scoring algorithms | Installing conda environments | Getting started | On-targeting efficiency scores | Cas9 methods | Rule Set 1 | Rule Set 3 | DeepHF | CRISPRscan | CRISPRater | Cas12a methods | enPAM+GB score | Cas13d methods | CasRxRF | Off-target specificity scores | MIT score | CFD score | Indel prediction score | Lindel score (Cas9) | License | Reproducibility | References

Introduction | Installation | Terminology | CRISPRko design | Nuclease specification | Target DNA specification | Designing spacer sequences | Sequence features characterization | Off-target search | Iterative spacer alignments | Faster alignment by removing repeat elements | Off-target scoring | On-target scoring | Restriction enzymes | Gene annotation | TSS annotation | SNP information | Filtering and ranking gRNAs | CRISPRa/CRISPRi design | CRISPR base editing with BE4max | CRISPR knockdown with Cas13d | Design for optical pooled screening (OPS) | Design of gRNA pairs with the PairedGuideSet object | Miscellaneous design use cases | Design with custom sequences | Off-target search in custom sequences | Adding non-targeting controls (NTCs) | Session Info | References

Introduction | Defining the base editor object | Designing spacer sequences | Allele prediction | gRNA-level aggregate variant scores | Session Info | References

Overview | Installation | Software requirements | OS Requirements | Getting started | Nuclease class | Examples | Accessor functions | CrisprNuclease class | CrisprNuclease objects provided in CrisprBase | CRISPR arithmetics | CRISPR terminology | Cut site | Obtaining spacer and PAM sequences from target sequences | Obtaining genomic coordinates of protospacer sequences using PAM site coordinates | BaseEditor class | CrisprNickase class | RNA-targeting nucleases | Additional notes | dCas9 and other "dead" nucleases | License | Reproducibility | References

Introduction | Installation | Creating self-contained Shiny applications | Basic GuideSet (no additional annotations) | Fully-annotated GuideSet | On-targets table | gRNA filters | Nucleotide content | Off-target count | Scores | Genomic Features | Isoform-specific parameters | Promoter targeting parameters | Visualizing on-targets | gRNA-specific anntations/list columns | On- and Off-targets | Gene Annotation | TSS Annotation | Restriction Enzyme | SNPs | Customized apps using Shiny modules | Session Info

Introduction | Example dataset | Creating your own dataset visualization | Step 1: creating a RGChannelSet object with minfi | Step 2: creating a shinyMethylSet object | Step 3: launching the interactive shiny interface | How to use the different \Biocpkg{shinyMethyl} panels | Advanced option: visualization of normalized data | What does a shinyMethylSet contain? | Figures | Quality control figure | Array design panel | Sex prediction algorithm panel | Principal Component Analysis (PCA) | Type I/II probe bias | Comparison of raw and normalized data | Visualization of batch effects in the TCGA HNSCC dataset | Visualization of cancer/normal differences in the TCGA HNSCC dataset | Session info | References

Installation and getting started | Components | Reproducibility

Introduction | Installation and getting started | Software requirements | OS Requirements | Installation from Bioconductor | Use cases | Visualizing the best gRNAs for a given gene | Plotting for precision targeting | CRISPRa and adding genomic annotations | Comparing multiple GuideSets targeting the same region | Setting plot size | Session Info

Overview of crisprBwa | Installation and getting started | Software requirements | OS Requirements | R Dependencies | Installation from Bioconductor | Building a bwa index | Alignment using runCrisprBwa | Applications beyond CRISPR | Example using RNAi (siRNA design) | Reproducibility | References

Overview of crisprBowtie | Installation and getting started | Software requirements | OS Requirements | Installation from Bioconductor | Building a bowtie index | Alignment using runCrisprBowtie | Applications beyond CRISPR | Example using RNAi (siRNA design) | Reproducibility | References

Installation from Bioconductor | Exploring the different data in crisprScoreData

Introduction | Installation | Overview | Build a reference index with bwa_build_index | Aligment with bwa_aln | Creating a SAM file | Creating a SAM file with secondary alignments | Aligment with bwa_mem | Session info | References