load_species_anno_db

Use <code>AnnotationHub</code> to load species-specific GTF and 2bit DNA
sequences. This function currently works for human, rat, and mouse.
The function will return:<ul>
<li><code>$gtf</code>: A <code>GRanges</code> object containing the GTF information</li>
<li><code>$tx.db</code>: A <code>tx.db</code> object made from the GTF</li>
<li><code>$dna</code>: The 2bit DNA sequence as a <code>DNAStringSet</code></li>
</ul>

On-target gene knockdown using siRNA ideally results from binding
fully complementary regions in mRNA transcripts to induce cleavage.
Off-target siRNA gene knockdown can occur through several modes, one being
a seed-mediated mechanism mimicking miRNA gene regulation. Seed-mediated
off-target effects occur when the ~8 nucleotides at the 5’ end of the guide
strand, called a seed region, bind the 3’ untranslated regions of mRNA,
causing reduced translation. Experiments using siRNA knockdown paired with
RNA-seq can be used to detect siRNA sequences with potential off-target
effects driven by the seed region. 'SeedMatchR' provides tools for exploring
and detecting potential seed-mediated off-target effects of siRNA in RNA-seq
experiments. 'SeedMatchR' is designed to extend current differential
expression analysis tools, such as 'DESeq2', by annotating results with
predicted seed matches. Using publicly available data, we demonstrate the
ability of 'SeedMatchR' to detect cumulative changes in differential gene
expression attributed to siRNA seed regions.

Tareian Cazares

SeedMatchR

Find Matches to Canonical SiRNA Seeds in Genomic Features

Gulcin Ozer

Jibo Wang

Rick Higgs

Eli Lilly and Company 

load_species_anno_db function

<dl><dt>species.name</dt>
<dd>Species name. Options: human, rat, mouse</dd>
<dt>remove.na.rows</dt>
<dd>Remove rows with NA in the gene_id column</dd></dl>

Arguments

Load species specific AnnotationDb — load_species_anno_db

<dl>

<dt>species.name</dt>
<dd>Species name. Options: human, rat, mouse</dd>


<dt>remove.na.rows</dt>
<dd>Remove rows with NA in the gene_id column</dd>

</dl>

load_species_anno_db: Load species specific `AnnotationDb`

Description

Usage

Value

Arguments

Examples