MiniLibCas9_Library: Genome-wide annotation for the MiniLibCas9 sgRNA library

In francescojm/CRISPRcleanR: Unsupervised correction of gene independent cell responses to CRISPR-cas9 targeting

Genome-wide annotation for the MiniLibCas9 sgRNA library

Description

A data frame with a named row for each sgRNA of the MiniLibCas9 sgRNA library [1] including annotations such as targeted genes, and genomic coordinates.

Usage

data("MiniLibCas9_Library")

Format

A data frame with 37701 observations on the following variables (among others).

CODE

alphanumerical identifier of the sgRNAs;

GENES

targeted gene;

STARTpos

starting genomic coordinate of the targeted genomic region (numeric);

STRAND

targeted DNA strand ('+' or '-')

CHRM

chromosome of where the targeted region resides (string)

ENDpos

ending genomic coordinate of the targeted genomic region (numeric).

seq

nucelotidic sequence of the sgRNAs without the PAM. (string).

Source

https://github.com/EmanuelGoncalves/crispy/blob/master/notebooks/minlib/libraries/MinLibCas9.csv.gz

References

[1] Goncalves E, Thomas M, Behan FM, Picco G, Pacini C, Allen F, Parry-Smith D, et al. 2019. Minimal Genome-Wide Human CRISPR-Cas9 Library. BioRxiv, January, 848895. https://doi.org/10.1101/848895

Examples

## Not run: 
## Loading sgRNA MiniLibCas9 library annotation file
data(MiniLibCas9_Library)
## Visualising first entries
head(MiniLibCas9_Library)

## Deriving the path of an example count file
## from screening the HT-29 cell line with the Brunello library
## [1]

fn<-paste(system.file('extdata', package = 'CRISPRcleanR'),
          '/HT29-MiniLibCas9_counts.tsv',sep='')

expName<-'HT29-MiniLibCas9'

## Loading, median-normalizing and computing fold-changes
normANDfcs<-
    ccr.NormfoldChanges(filename = fn,
                        display = TRUE,
                        min_reads = 30,
                        EXPname = expName,
                        libraryAnnotation = MiniLibCas9_Library)

## Genome-sorting the fold changes
gwSortedFCs<-
    ccr.logFCs2chromPos(foldchanges = normANDfcs$logFCs,
                        libraryAnnotation = MiniLibCas9_Library)

## Identifying and correcting biased sgRNAs' fold changes
correctedFCs_and_segments<-
    ccr.GWclean(gwSortedFCs = gwSortedFCs,
                display=TRUE,
                label=expName)

## End(Not run)

francescojm/CRISPRcleanR documentation built on April 30, 2023, 5:41 a.m.