DESCRIPTION

Package: ReferenceEnhancer
Title: Package For Optimizing And Assembling Genome Annotations For 3’ Single-Cell RNA-Sequencing Analysis
Version: 0.9
Authors@R: 
    person("Helen", "Poldsam", , "helen.poldsam@utsouthwestern.edu", role = c("aut", "cre"))
    person("Allan-Hermann", "Pool", , "allan-hermann.pool@utsouthwestern.edu", role = c("aut", "cre"))
Description: ReferenceEnhancer contains a set of tools for optimizing genome annotations for droplet based 3’ single-cell RNA-sequencing (10x Genomics, Dropseq etc.) data analysis. Regular genome annotations and transcriptomic references generated based on them come with several problems causing discarded sequencing data from final gene expression estimates (outlined in detail in https://www.biorxiv.org/content/10.1101/2022.04.26.489449v1). These include read loss stemming from gene overlaps, sequencing reads mapping to 3’ unannoated exons as well as introns. ReferenceEnhancer enables fixing these issues and assembling optimized genome annotations that circumvent these problems and recover the discarded gene expression data.
URL: https://github.com/PoolLab/ReferenceEnhancer 
License: Artistic-2.0
Encoding: UTF-8
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.2.3
Imports: 
    gdata,
    GenomicAlignments,
    GenomicRanges,
    IRanges,
    readr,
    Rsamtools,
    rtracklayer,
    stringr