IntEREst

Intron-Exon Retention Estimator

Bioconductor version: 3.23 · Package version: 1.36.0

This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).

Installation

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("IntEREst")

Maintainer	Ali Oghabian <Ali.Oghabian@Helsinki.Fi>
Author	Ali Oghabian <Ali.Oghabian@Helsinki.Fi>, Dario Greco <dario.greco@helsinki.fi>, Mikko Frilander <Mikko.Frilander@helsinki.fi>
License	GPL-2
Downloads rank	368
Source branch	RELEASE_3_23
biocViews	Alignment, AlternativeSplicing, Coverage, DifferentialExpression, DifferentialSplicing, ImmunoOncology, Normalization, RNASeq, Sequencing, Software

Dependencies

Depends: R (>= 3.5.0), GenomicRanges, Rsamtools, SummarizedExperiment, edgeR, S4Vectors, GenomicFiles

Imports: seqLogo, Biostrings, GenomicFeatures (>= 1.39.4), txdbmaker, IRanges, seqinr, graphics, grDevices, stats, utils, grid, methods, DBI, RMariaDB, GenomicAlignments, BiocParallel, BiocGenerics, DEXSeq, DESeq2

Suggests: clinfun, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19