README.Rmd

---
title: "crisprDesignData: useful data for the crisprVerse ecosystem"
output: 
  github_document:
    toc: true
---

[![R-CMD-check](https://github.com/crisprVerse/crisprDesignData/actions/workflows/check-standard.yaml/badge.svg)](https://github.com/crisprVerse/crisprDesignData/actions/workflows/check-standard.yaml)

```{r, echo=FALSE, results="hide"}
options("knitr.graphics.auto_pdf"=TRUE)
```

Authors: Jean-Philippe Fortin, Luke Hoberecht


# Overview

The `crisprDesignData` package provides ready-to-use 
annotation data needed needed for the [crisprVerse](https://github.com/crisprVerse) ecosystem, 
for both human and human. Visit our [crisprVerse tutorial page](https://github.com/crisprVerse/Tutorials) to learn how the data are used for performing CRISPR gRNA design. 

# Installation

## Software requirements

### OS Requirements

This package is supported for macOS, Linux and Windows machines.
It was developed and tested on R version 4.2.1.

## Installation

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

```r
install.packages("devtools")
devtools::install_github("crisprVerse/crisprDesignData")
```


### Getting started

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

```{r, warnings=FALSE, message=FALSE}
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) |
| `canonicalHuman`   | `data.frame` |   Release 104          | Canonical Ensembl transcripts for human |
| `canonicalMouse`   | `data.frame` |   Release 102          | Canonical Ensembl transcripts for mouse |
| `pfamTableHuman`   | `DataFrame` |   Release 104          | Pfam domains for human Ensembl transcripts |
| `pfamTableMousen`   | `DataFrame` |   Release 102          | Pfam domains for mouse Ensembl transcripts |



# 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.R`in 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:

```{r, warning=FALSE, message=FALSE}
data(txdb_human, package="crisprDesignData")
```

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

```{r, warning=FALSE, message=FALSE}
head(S4Vectors::metadata(txdb_human))
```

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

```{r}
names(txdb_human)
```

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

```{r}
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:


```{r, warning=FALSE, message=FALSE}
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.R`in the `inst` folder to see how to generate such data.

Let's take a look at `tss_human`:

```{r}
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:

```{r, warning=FALSE, message=FALSE}
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.R`in the `inst` folder to see how to generate such data.
The names of the `DNAStringSet` are Ensembl transcript IDs:


```{r}
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:

```{r}
data(gr.repeats.hg38, package="crisprDesignData")
head(gr.repeats.hg38)
```

# Canonical transcripts

The data.frames `canonicalHuman` and `canonicalMouse` contains information
about Ensembl canonical transcripts for human and mouse respectively.
The Ensembl canonical transcript is the best well-supported, 
biologically representative, highly expressed, and highly conserved transcript
for a given gene. MANE Select is used as the canonical transcript for 
human protein coding genes where available.

```{r}
data(canonicalHuman, package="crisprDesignData")
head(canonicalHuman)
```

# Pfam domains

The DataFrame objects `pfamTableHuman` and `pfamTableMouse` contains 
Pfam domains retrieved from biomaRt for human and mouse transcripts.


```{r}
data(pfamTableHuman, package="crisprDesignData")
head(pfamTableHuman)
```

The `pfam_start` and `pfam_end` columns contain the amino acid coordinates
of the domain start and end, respectively, and the `pfam` column contains
the Pfam domain ID. 



# License

The package is licensed under the MIT license. 

# Reproducibility

```{r}
sessionInfo()
```