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raer

Characterize A-to-I RNA editing in bulk and single-cell RNA sequencing experiments

https://github.com/rnabioco/raer

Science Score: 57.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 9 DOI reference(s) in README
  • ○
    Academic publication links
  • ✓
    Committers with academic emails
    5 of 9 committers (55.6%) from academic institutions
  • ✓
    Institutional organization owner
    Organization rnabioco has institutional domain (medschool.cuanschutz.edu)
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (15.8%) to scientific vocabulary

Keywords

bioconductor-package rna-seq-analysis single-cell-analysis single-cell-rna-seq

Keywords from Contributors

rna-seq genomics assign-identities clusters marker-genes gene
Last synced: 6 months ago · JSON representation

Repository

Characterize A-to-I RNA editing in bulk and single-cell RNA sequencing experiments

Basic Info
Statistics
  • Stars: 8
  • Watchers: 4
  • Forks: 2
  • Open Issues: 2
  • Releases: 1
Topics
bioconductor-package rna-seq-analysis single-cell-analysis single-cell-rna-seq
Created over 4 years ago · Last pushed 8 months ago
Metadata Files
Readme Changelog License

README.Rmd 

---
output: github_document
---



```{r, include = FALSE}
knitr::opts_chunk$set(
    collapse = TRUE,
    comment = "#>",
    fig.path = "man/figures/README-",
    out.width = "100%"
)
```

# raer 


[![R-CMD-check-bioc](https://github.com/rnabioco/raer/actions/workflows/check-bioc.yml/badge.svg)](https://github.com/rnabioco/raer/actions/workflows/check-bioc.yml)
[![Codecov test coverage](https://codecov.io/gh/rnabioco/raer/branch/devel/graph/badge.svg)](https://app.codecov.io/gh/rnabioco/raer?branch=devel)
[![platforms](https://bioconductor.org/shields/availability/devel/raer.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/raer)
[![bioc](https://bioconductor.org/shields/years-in-bioc/raer.svg)](https://bioconductor.org/packages/release/bioc/html/raer.html)


raer facilitates analysis of RNA adenosine editing in the
[Bioconductor](https://bioconductor.org/) ecosystem.

## Installation

`raer` is available on [Bioconductor](https://bioconductor.org/packages/release/bioc/html/raer.html):

```{r, eval = FALSE}
if (!require("BiocManager", quietly = TRUE)) {
    install.packages("BiocManager")
}

BiocManager::install("raer")
```

You can install the development version of raer from [GitHub](https://github.com/rnabioco/raer) with:

```{r, eval = FALSE}
BiocManager::install("rnabioco/raer")
```

## Quick start

![raer workflow overview](man/figures/raer_workflow.png)

raer provides methods to compute per site read count summaries from BAM
alignment files, either for known editing sites, or for all detected sites.

```{r pileup_sites}
library(raer)
bam1fn <- raer_example("SRR5564269_Aligned.sortedByCoord.out.md.bam")
bam2fn <- raer_example("SRR5564277_Aligned.sortedByCoord.out.md.bam")
fafn <- raer_example("human.fasta")

bams <- c("ko" = bam1fn, "wt" = bam2fn)

rse <- pileup_sites(bams, fafn)
```


To facilitate comparisons across groups, base count data and genomic coordinates 
are stored in a  `RangedSummarizedExperiment`. 

```{r}
suppressMessages(library(SummarizedExperiment))
rse
assays(rse)
colData(rse)
```

```{r}
assays(rse)$nRef[1:4, ]
assays(rse)$nAlt[1:4, ]
```


The `FilterParam()` class holds multiple options for customizing the output of `pileup_sites()`.

```{r params}
fp <- FilterParam(
    only_keep_variants = TRUE,
    library_type = "fr-first-strand",
    min_depth = 2
)

rse <- pileup_sites(bams, fafn, param = fp)
rse
```

`pileup_cells()` provides support for quantifying editing sites in single cell libraries.

```{r scrnaseq}
scbam_fn <- raer_example("5k_neuron_mouse_possort.bam")
outdir <- tempdir()

editing_sites <- GRanges(
    c(
        "2:579:-",
        "2:625:-",
        "2:589:-"
    ),
    REF = "A",
    ALT = "G"
)

cbs <- c(
    "CACCAAACAACAACAA-1",
    "TATTCCACACCCTCTA-1",
    "GACCTTCAGTTGTAAG-1"
)

sce <- pileup_cells(scbam_fn,
    sites = editing_sites,
    cell_barcodes = cbs,
    param = fp,
    output_directory = outdir
)
sce
```

```{r}
assays(sce)$nRef
assays(sce)$nAlt
```

## Related work

Core routines in `raer` are implemented using the `htslib` library and methods from `samtools` and `bcftools`. `raer` builds off of approaches from other RNA editing detection tools:  

 - [REDItools](https://github.com/BioinfoUNIBA/REDItools) from [Picardi E, Pesole G](https://doi.org/10.1093/bioinformatics/btt287)   
 - [JACUSA2](https://github.com/dieterich-lab/JACUSA2)  from [Piechotta M et al ](https://doi.org/10.1186/s12859-016-1432-8)    
 - [deNovo-Detect](https://github.com/a2iEditing/deNovo-Detect) from [Gabay O et al ](https://doi.org/10.1038/s41467-022-28841-4)   
 - [RNAEditingIndexer](https://github.com/a2iEditing/RNAEditingIndexer) from [Roth SH et al](https://doi.org/10.1038/s41592-019-0610-9)  
- [SAILOR](https://github.com/YeoLab/sailor) from [Washburn MC et al](https://10.1016/j.celrep.2014.01.011)

Owner

  • Name: RNA Bioscience Initiative (RBI)
  • Login: rnabioco
  • Kind: organization
  • Email: jay.hesselberth@cuanschutz.edu
  • Location: University of Colorado School of Medicine

The RNA Bioscience Initiative Informatics Fellows program

GitHub Events

Total
  • Watch event: 1
  • Delete event: 1
  • Push event: 9
  • Pull request event: 4
  • Create event: 3
Last Year
  • Watch event: 1
  • Delete event: 1
  • Push event: 9
  • Pull request event: 4
  • Create event: 3

Committers

Last synced: 6 months ago

All Time
  • Total Commits: 317
  • Total Committers: 9
  • Avg Commits per committer: 35.222
  • Development Distribution Score (DDS): 0.293
Past Year
  • Commits: 8
  • Committers: 5
  • Avg Commits per committer: 1.6
  • Development Distribution Score (DDS): 0.75
Top Committers
Name Email Commits
Kent Riemondy k****y@g****m 224
Jay Hesselberth j****h@g****m 35
Jay Hesselberth j****h@c****u 28
Kristen Wells k****s@c****u 16
rmsheridan r****n@u****u 5
J Wokaty j****y@s****u 4
A Wokaty a****y@s****u 2
J Wokaty j****y@u****m 2
kriemo k****o@K****l 1
Committer Domains (Top 20 + Academic)
sph.cuny.edu: 2 cuanschutz.edu: 2 ucdenver.edu: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 37
  • Total pull requests: 67
  • Average time to close issues: 4 months
  • Average time to close pull requests: 2 days
  • Total issue authors: 4
  • Total pull request authors: 4
  • Average comments per issue: 1.14
  • Average comments per pull request: 0.27
  • Merged pull requests: 63
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 1
  • Pull requests: 2
  • Average time to close issues: about 11 hours
  • Average time to close pull requests: 27 minutes
  • Issue authors: 1
  • Pull request authors: 1
  • Average comments per issue: 3.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • kriemo (18)
  • jayhesselberth (15)
  • shmmuzhangh (2)
  • sheridar (1)
Pull Request Authors
  • kriemo (51)
  • jayhesselberth (16)
  • sheridar (1)
  • kwells4 (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 4,426 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 5
  • Total maintainers: 1
bioconductor.org: raer

RNA editing tools in R

  • Versions: 5
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 4,426 Total
Rankings
Dependent repos count: 0.0%
Stargazers count: 16.8%
Forks count: 17.6%
Dependent packages count: 31.7%
Average: 33.0%
Downloads: 99.0%
Maintainers (1)
kent.riemondy@gmail.com
Last synced: 7 months ago

Dependencies

DESCRIPTION cran
  • BSgenome * imports
  • BiocGenerics * imports
  • BiocParallel * imports
  • Biostrings * imports
  • GenomeInfoDb * imports
  • GenomicAlignments * imports
  • GenomicFeatures * imports
  • GenomicRanges * imports
  • IRanges * imports
  • Matrix * imports
  • R.utils * imports
  • Rcpp * imports
  • Rsamtools * imports
  • S4Vectors * imports
  • SummarizedExperiment * imports
  • data.table * imports
  • fastmap * imports
  • methods * imports
  • rtracklayer * imports
  • stats * imports
  • stringr * imports
  • utils * imports
  • zlibbioc * imports
  • AnnotationHub * suggests
  • BiocStyle * suggests
  • ComplexHeatmap * suggests
  • DESeq2 * suggests
  • RColorBrewer * suggests
  • SNPlocs.Hsapiens.dbSNP144.GRCh38 * suggests
  • SingleCellExperiment * suggests
  • TxDb.Hsapiens.UCSC.hg38.knownGene * suggests
  • edgeR * suggests
  • knitr * suggests
  • limma * suggests
  • rmarkdown * suggests
  • scater * suggests
  • testthat * suggests
  • viridis * suggests
.github/workflows/check-bioc.yml actions
  • JamesIves/github-pages-deploy-action releases/v4 composite
  • actions/cache v3 composite
  • actions/checkout v3 composite
  • actions/upload-artifact master composite
  • docker/build-push-action v1 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite