Bioconductor Crisprbase
Provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base...
Install
npx skills add bioMate-AI/biomate-bioconductor-kb --skill bioconductor-crisprbase -g -a claude-code -y- Repository
- bioMate-AI/biomate-bioconductor-kb793
- Category
- Engineering
- Updated
- 5mo ago
- License
- See repository
- Context cost
- Lightabout 1,329 tokens
- Runs scripts
- No, instructions only
What it does
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.
crisprBase
Workflows
Standard Workflow
Define and manipulate S4 classes representing restriction enzymes, CRISPR nucleases, base editors, and nickases.
library(crisprBase)
# 1. Define SpCas9 Nuclease (3' PAM)
SpCas9 <- CrisprNuclease(
"SpCas9",
targetType = "DNA",
pams = c("(3/3)NGG", "(3/3)NAG", "(3/3)NGA"),
weights = c(1, 0.2593, 0.0694),
pam_side = "3prime",
spacer_length = 20
)
# 2. Define AsCas12a Nuclease (5' PAM)
AsCas12a <- CrisprNuclease(
"AsCas12a",
targetType = "DNA",
pams = "TTTV(18/23)",
pam_side = "5prime",
spacer_length = 23
)
# 3. Define a Cytosine Base Editor (BE4max) with custom editing weights
weightsFile <- system.file("be/b4max.csv", package = "crisprBase", mustWork = TRUE)
ws <- t(read.csv(weightsFile))
ws <- as.data.frame(ws)
colnames(ws) <- ws["Position", ]
ws <- ws[-c(match("Position", rownames(ws))), , drop = FALSE]
ws <- as.matrix(ws)
BE4max <- BaseEditor(
SpCas9,
baseEditorName = "BE4max",
editingStrand = "original",
editingWeights = ws,
scale = TRUE
)
# 4. Define CRISPR Nickases (Cas9D10A)
Cas9D10A <- CrisprNickase(
"Cas9D10A",
nickingStrand = "opposite",
pams = c("(3)NGG", "(3)NAG", "(3)NGA"),
weights = c(1, 0.2593, 0.0694),
pam_side = "3prime",
spacer_length = 20
)
Note on inputs/outputs: Input is nuclease specifications and weight files; output is S4 objects representing custom CRISPR nucleases, base editors, and nickases.
