easyRNASeq
Count summarization and normalization for RNA-Seq data
Bioconductor version: 3.23 · Package version: 2.48.0
Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq' or 'edgeR' package.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("easyRNASeq")Details
| Maintainer | Nicolas Delhomme <nicolas.delhomme@umu.se> |
| Author | Nicolas Delhomme, Ismael Padioleau, Bastian Schiffthaler, Niklas Maehler |
| License | Artistic-2.0 |
| Downloads rank | 673 |
| Source branch | RELEASE_3_23 |
| biocViews | GeneExpression, Genetics, ImmunoOncology, Preprocessing, RNASeq, Software |
Documentation
- A walkthrough the easyRNASeq package functionalities
- R / Bioconductor for High Throughput Sequence Analysis
Download
Follow the installation instructions to use this package in your R session.
| Source package | easyRNASeq_2.48.0.tar.gz |
| Windows binary (x86_64) | easyRNASeq_2.48.0.zip |
| macOS binary (arm64) | easyRNASeq_2.48.0.tgz |
| macOS binary (x86_64) | easyRNASeq_2.48.0.tgz |
Dependencies
Imports: Biobase (>= 2.64.0), BiocFileCache (>= 2.12.0), BiocGenerics (>= 0.50.0), BiocParallel (>= 1.38.0), biomaRt (>= 2.60.1), Biostrings (>= 2.77.2), edgeR (>= 4.2.1), Seqinfo, genomeIntervals (>= 1.60.0), GenomicAlignments (>= 1.45.1), GenomicRanges (>= 1.61.1), SummarizedExperiment (>= 1.39.1), graphics, IRanges (>= 2.38.1), LSD (>= 4.1-0), methods, parallel, rappdirs (>= 0.3.3), Rsamtools (>= 2.25.1), S4Vectors (>= 0.42.1), ShortRead (>= 1.62.0), utils
Suggests: BiocStyle (>= 2.32.1), BSgenome (>= 1.72.0), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0), curl, knitr, rmarkdown, RUnit (>= 0.4.33)
Reverse dependencies
Imports Me (1): msgbsR