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derfinder
Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution
Bioconductor version: 3.0
Annotation-agnostic differential expression analysis of RNA-seq data by calculating F-statistics at base-pair resolution
Author: Leonardo Collado-Torres [aut, cre], Alyssa C. Frazee [aut], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]
Maintainer: Leonardo Collado-Torres <lcollado at jhu.edu>
Citation (from within R,
enter citation("derfinder")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("derfinder")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("derfinder")
| HTML | R Script | derfinder advanced details and usage |
| HTML | R Script | Introduction to derfinder |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DifferentialExpression, RNASeq, Sequencing, Software |
| Version | 1.0.10 |
| In Bioconductor since | BioC 3.0 (R-3.1) |
| License | Artistic-2.0 |
| Depends | R (>= 3.1.1) |
| Imports | AnnotationDbi(>= 1.27.9), BiocParallel, bumphunter(>= 1.3.3), derfinderHelper(>= 1.0.0), GenomeInfoDb(>= 1.2.2), GenomicAlignments, GenomicFeatures, GenomicFiles, GenomicRanges(>= 1.17.40), Hmisc, IRanges(>= 1.99.28), qvalue, Rsamtools, rtracklayer, S4Vectors(>= 0.2.3) |
| LinkingTo | |
| Suggests | biovizBase, devtools (>= 1.6), derfinderData(>= 0.99.0), ggplot2, knitcitations (>= 1.0.1), knitr (>= 1.6), knitrBootstrap (>= 0.9.0), rmarkdown (>= 0.3.3), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/lcolladotor/derfinder |
| Depends On Me | |
| Imports Me | derfinderPlot, regionReport |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | derfinder_1.0.10.tar.gz |
| Windows Binary | derfinder_1.0.10.zip |
| Mac OS X 10.6 (Snow Leopard) | derfinder_1.0.10.tgz |
| Mac OS X 10.9 (Mavericks) | derfinder_1.0.10.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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