In Jfortin1/crisprDesignData: Precomputed data for crisprDesign

options("knitr.graphics.auto_pdf"=TRUE)

Authors: Jean-Philippe Fortin, Luke Hoberecht

Date: July 16, 2022

Overview

The crisprDesignData package provides ready-to-use annotation data needed needed for the crisprDesign ecosystem, for both human and human.

Installation

Software requirements

OS Requirements

This package is supported for macOS, Linux and Windows machines. It was developed and tested on R version 4.2.

Installation

crisprDesignData can be installed by typing the following commands inside of an R session:

install.packages("devtools")
devtools::install_github("Jfortin1/crisprDesignData")

Getting started

crisprDesignData can be loaded into an R session in the usual way:

library(crisprDesignData)

Datasets

| Object name | Object class | Version | Description | |----------- | ----------- | ----------- |----------- | | txdb_human | GRangesList | Release 104 | Ensembl gene model for human (hg38/GRCh38) | | txdb_mouse | GRangesList | Release 102 | Ensembl gene model for mouse (mm10/GRCm38) | | tss_human | GRanges | Release 104 | Ensembl-based TSS coordinates for human (hg38/GRCh38) | | tss_mouse | GRanges | Release 102 | Ensembl-based TSS coordinates for human (mm10/GRCm38) | | mrnasHuman | DNAStringSet | Release 104 | Ensembl-based mRNA nucleotide sequences for human (hg38/GRCh38) | | mrnasMouse | DNAStringSet | Release 102 | Ensembl-based mRNA nucleotide sequences for mouse (mm10/GRCm38) | | gr.repeats.hg38 | GRanges | | RepeatMasker data from UCSC genome browser (hg38/GRCh38) | | gr.repeats.mm10 | GRanges | | RepeatMasker data from UCSC genome browser (mm10/GRCm38) |

TxDb datasets

The txdb_human and txdb_mouse objects are GRangesList representing gene models for human and mouse, respectively, from Ensembl. They were constructed using the function getTxDb in crisprDesign. See the script generateTxDbData.Rin the inst folder to see how to generate such data for other organisms (internet connection needed).

Let's look at the txdb_human object. We first load the data:

data(txdb_human, package="crisprDesignData")

We can look at metadata information about the gene model by using the metadata function from the S4Vectors package:

head(S4Vectors::metadata(txdb_human))

The object is a GRangesList with 7 elements that contain genomic coordinates for different levels of the gene model:

names(txdb_human)

As an example, let's look at the GRanges containing genomic coordinates for all exons represented in the gene model:

txdb_human$exons

The function queryTxObject in crisprDesign is a user-friendly function to work with such objects, for instance once can return the CDS coordinates for the KRAS transcripts using the following lines of code:

library(crisprDesign)
cds <- queryTxObject(txdb_human,
                     featureType="cds",
                     queryColumn="gene_symbol",
                     queryValue="KRAS")
head(cds)

TSS datasets

The tss_human and tss_mouse objects are GRanges representing the transcription starting sites (TSSs) coordinates for human and mouse, respectively. The coordinates were extracted from the transcripts stored in the Ensembl-based models txdb_human and txdb_mouse using the function getTssObjectFromTxObject from crisprDesign. See the script generateTssObjects.Rin the inst folder to see how to generate such data.

Let's take a look at tss_human:

data(tss_human, package="crisprDesignData")
head(tss_human)

The function queryTss in crisprDesign is a user-friendly function to work with such objects, accepting an argument called tss_window to specify a number of nucleotides upstream and downstream of the TSS. This is particularly useful to return genomic regions to target for CRISPRa and CRISPRi.

For instance, if we want to target the region 500 nucleotides upstream of any of the KRAS TSSs, one can use the following lines of code:

library(crisprDesign)
tss <- queryTss(tss_human,
                queryColumn="gene_symbol",
                queryValue="KRAS",
                tss_window=c(-500,0))
head(tss)

mRNA datasets

The mrnasHuman and mrnasMouse objects are DNAStringSet storing the nucleotide sequence of mRNAs derived from the txdb_human and txdb_mouse gene models, respectively. It was obtained using the function getMrnaSequences from crisprDesign. See the script generateMrnaData.Rin the inst folder to see how to generate such data. The names of the DNAStringSet are Ensembl transcript IDs:

data(mrnasHuman, package="crisprDesignData")
data(mrnasMouse, package="crisprDesignData")
head(mrnasHuman)
head(mrnasMouse)

Those objects are particularly useful for gRNA design for RNA-targeting nucleases such as RfxCas13d (CasRx).

Repeats datasets

The objects gr.repeats.hg38 and gr.repeats.mm10 objects are GRanges representing the genomic coordinates of repeat elements in the human and mouse genomes, as defined by the RepeatMasker tracks in the UCSC genome browser.

Let's look at the repeats elements in the human genome:

data(gr.repeats.hg38, package="crisprDesignData")
head(gr.repeats.hg38)

License

The package is licensed under the MIT license.

Reproducibility

sessionInfo()

Jfortin1/crisprDesignData documentation built on Aug. 16, 2022, 4:44 p.m.