BioConductor

derfinder 1.14.0

Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach

Released Feb 23, 2018 by Leonardo Collado-Torres

This package cannot yet be used with Renjin it depends on other packages which are not available: rtracklayer 1.40.5, GenomicFiles 1.16.0, GenomicFeatures 1.32.2, and bumphunter 1.22.0

Dependencies

GenomicFiles 1.16.0 rtracklayer 1.40.5 bumphunter 1.22.0 GenomicFeatures 1.32.2 GenomeInfoDb 1.16.0 qvalue 2.12.0 Hmisc 4.1-1 S4Vectors 0.18.3 BiocParallel 1.14.2 Rsamtools 1.32.3 AnnotationDbi 1.42.1 GenomicAlignments 1.16.0 GenomicRanges 1.32.6 BiocGenerics 0.26.0 IRanges 2.14.10 derfinderHelper 1.14.0

This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.