| Title: | A collection of datasets for use with raer package |
|---|---|
| Description: | raerdata is an ExperimentHub package that provides a collection of files useful for demostrating functionality in the raer package. Datasets include 10x genomics scRNA-seq, bulk RNA-seq, and paired whole-genome and RNA-seq data. Additionally databases of human and mouse RNA editing sites are provided. |
| Authors: | Kent Riemondy [aut, cre] (ORCID: <https://orcid.org/0000-0003-0750-1273>) |
| Maintainer: | Kent Riemondy <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 1.11.0 |
| Built: | 2026-10-10 10:45:35 UTC |
| Source: | https://github.com/bioc/raerdata |
Study GSE99249 examined RNA editing in WT, ADAR1KO, and ADAR1-p150 HEK293T cells treated with and without interferon beta.
GSE99249()GSE99249()
GSE99249() will download BAM and BAM index files from 6 RNA-seq
libraries. 3 libraries are ADAR1 knockout cells treated with interferon
beta and 3 libraries are wild type cells treated with interferon beta.
The BAM files contain alignments from chromosome 18.
A list containing:
bams A BamFileList object, indicating the BAM file paths and
BAI indexes.
fasta A path to a fasta file from chr18 of hg38
snps a GRanges object containing known SNPs from the REDIportal
database (hg38)
GSE99249()GSE99249()
Whole genome and RNA sequencing data from NA12878 cell line
NA12878()NA12878()
Will download BAM and BAM index files from whole genome and RNA sequencing of the NA12878 cell line, The data is from the first megabase of chromosome 4. Additionally a fasta file and a database of known SNPs will be downloaded.
A list containing:
bams A BamFileList object, indicating the BAM file paths and
BAI indexes.
fasta A path to a fasta file containing the genome sequence of
the first megabase of chr4 (hg38)
snps a GRanges object containing SNPs from the first megabase
of chr4
NA12878()NA12878()
A 10x Genomics 3' single cell RNA-seq library from 10k PBMCs. The BAM file contains alignments from chr16. A SingleCellExperiment is also provided with pre-processed gene expression data, a UMAP projection and cell type annotations.
pbmc_10x()pbmc_10x()
pbmc_10x() will download a BAM, BAM index file, REDIportal RNA editing
sites, and a SingleCellExperiment object from the ExperimentHub.
A list containing:
bam a BamFile object indicating the BAM and BAI file paths.
Contains alignments from only chr16 (hg38).
sites a GRanges object containing known RNA editing sites from
the REDIportal database (hg38).
sce a SingleCellExperiment object containing gene expression
data, a UMAP projection and cell type annotations.
pbmc_10x()pbmc_10x()
A collection of datasets and databases to demonstrate RNA-editing analysis approaches using the raer package.
atlases
a collection of RNA editing databases
NA12878
Whole genome and RNA sequencing data from the NA12878 cell line
GSE99249
RNA sequencing data from a study that examined RNA editing in
WT, ADAR1KO, and ADAR1-p150 HEK293T cells treated with and without
interferon beta.
pbmc_10x single cell RNA sequencing data from human PBMCs from
10x Genomics
Databases of known RNA editing sites
rediportal_full_mm10() rediportal_coords_mm10() rediportal_full_hg38() rediportal_coords_hg38() gabay_sites_mm10() gabay_sites_hg38()rediportal_full_mm10() rediportal_coords_mm10() rediportal_full_hg38() rediportal_coords_hg38() gabay_sites_mm10() gabay_sites_hg38()
rediportal_full_hg38() will download the human REDIportal database for
hg38 which has been converted into a GRanges object. The GRanges is
supplemented with additional columns of information provided by the
REDIportal database, including gene location, repeat type, dbSNP
annotation, and potential for amino-acid recoding.
rediportal_coords_hg38() will download the human REDIportal database for
hg38 which has been converted into a GRanges object, which only
contains the coordinates of the editing site.
rediportal_full_mm10() will download the mouse REDIportal database for
mm10 which has been converted into a GRanges object. The GRanges is
supplemented with additional columns of information provided by the
REDIportal database, including gene location, repeat type, dbSNP
annotation, and potential for amino-acid recoding.
rediportal_coords_mm10()will download the mouse REDIportal database for
mm10 which has been converted into a GRanges object, which only contains the
coordinates of the editing site.
gabay_sites_hg38() will download high-confidence human CDS editing sites
(hg38).
gabay_sites_mm10() will download high-confidence mouse CDS editing sites
(lifted-over from hg38 to mm10).
A GRanges object.
gabay_sites_hg38()gabay_sites_hg38()