derfinder protocols

View derfinder computational protocol

derfinder statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Differential expression Normalization chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

derfinder specifications

Information


Unique identifier OMICS_02208
Name derfinder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.14.0
Stability Stable
Requirements
limma, methods, testthat, rtracklayer, GenomicAlignments, ggplot2, BiocParallel, DESeq2, GenomicFeatures, R(>=3.2), TxDb.Hsapiens.UCSC.hg19.knownGene, Hmisc, biovizBase, AnnotationDbi(>=1.27.9), BiocGenerics(>=0.25.1), bumphunter(>=1.9.2), derfinderHelper(>=1.1.0), GenomeInfoDb(>=1.3.3), GenomicFiles, GenomicRanges(>=1.17.40), IRanges(>=2.3.23), qvalue(>=1.99.0), Rsamtools(>=1.25.0), S4Vectors(>=0.9.38), BiocStyle(>=2.5.19), devtools(>=1.6), derfinderData(>=0.99.0), derfinderPlot, knitcitations(>=1.0.1), knitr(>=1.6), RefManageR, rmarkdown(>=0.3.3)
Maintained Yes

Versioning


Add your version

Documentation


Maintainer


  • person_outline Leonardo Collado-Torres <>

Publications for derfinder

derfinder in pipeline

2014
PMCID: 4281298
PMID: 25501035
DOI: 10.1038/nn.3898

[…] in the software) . the total number of aligned reads across the autosomal and sex chromosomes (dropping reads mapping to the mitochondria chromosome) per sample are provided in ., we implemented the derfinder pipeline available from http://bioconductor.org/packages/release/bioc/html/derfinder.html on the 36 discovery samples () base-level coverage data (the number of reads crossing each base […]


To access a full list of citations, you will need to upgrade to our premium service.

derfinder in publication

PMCID: 4281298
PMID: 25501035
DOI: 10.1038/nn.3898

[…] adult and elderly () – and implemented an annotation-agnostic differential expression analysis to leverage the power of rna-seq without the difficulties of transcript assembly . this method, called derfinder, identifies differential expression at base-pair resolution, and forms differentially expressed regions (ders) by joining adjacent differentially expressed bases. we tested for differences […]


To access a full list of publications, you will need to upgrade to our premium service.

derfinder reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review derfinder