Package: derfinder 1.39.0

Leonardo Collado-Torres

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

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.

Authors:Leonardo Collado-Torres [aut, cre], Alyssa C. Frazee [ctb], Andrew E. Jaffe [aut], Jeffrey T. Leek [aut, ths]

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derfinder.pdf |derfinder.html✨
derfinder/json (API)
NEWS

# Install 'derfinder' in R:

install.packages('derfinder', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lcolladotor/derfinder/issues

Datasets:

genomeData - Genome samples processed data
genomeDataRaw - Genome samples processed data
genomeFstats - F-statistics for the example data
genomeInfo - Genome samples information
genomeRegions - Candidate DERs for example data
genomicState - Genomic State for Hsapiens.UCSC.hg19.knownGene

On BioConductor:derfinder-1.39.0(bioc 3.20)derfinder-1.38.0(bioc 3.19)

bioconductor-package

26 exports 2.35 score 134 dependencies 7 dependents 6 mentions

Last updated 2 months agofrom:f9cd986e0c

Exports:advancedArg analyzeChr annotateRegions calculatePvalues calculateStats coerceGR collapseFullCoverage coverageToExon createBw createBwSample define_cluster extendedMapSeqlevels filterData findRegions fullCoverage getRegionCoverage getTotalMapped loadCoverage makeGenomicState makeModels mergeResults preprocessCoverage railMatrix rawFiles regionMatrix sampleDepth

Dependencies:abind AnnotationDbi askpass backports base64enc BH Biobase BiocGenerics BiocIO BiocParallel Biostrings bit bit64 bitops blob BSgenome bslib bumphunter cachem checkmate cli cluster codetools colorspace cpp11 crayon curl data.table DBI DelayedArray derfinderHelper digest doRNG evaluate fansi farver fastmap fontawesome foreach foreign formatR Formula fs futile.logger futile.options GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges ggplot2 glue gridExtra gtable highr Hmisc htmlTable htmltools htmlwidgets httr IRanges isoband iterators jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl pillar pkgconfig plogr plyr png qvalue R6 rappdirs RColorBrewer Rcpp RCurl reshape2 restfulr Rhtslib rjson rlang rmarkdown rngtools rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tinytex UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML XVector yaml zlibbioc

derfinder quick start guide

Leonardo Collado-Torres

Rendered fromderfinder-quickstart.Rmdusingknitr::rmarkdownon Jun 18 2024.

Last update: 2021-05-02
Started: 2015-12-09

derfinder users guide

Leonardo Collado-Torres

Rendered fromderfinder-users-guide.Rmdusingknitr::rmarkdownon Jun 18 2024.

Last update: 2020-12-17
Started: 2015-11-11

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Run the derfinder analysis on a chromosome	analyzeChr
Assign genomic states to regions	annotateRegions
Calculate p-values and identify regions	calculatePvalues
Calculate F-statistics at base pair resolution from a loaded BAM files	calculateStats
Coerce the coverage to a GRanges object for a given sample	coerceGR
Collapse full coverage information for efficient quantile computations	collapseFullCoverage
Extract coverage information for exons	coverageToExon
Export coverage to BigWig files	createBw
Create a BigWig file with the coverage information for a given sample	createBwSample
Define a cluster to use.	define_cluster
Deprecated functions in package 'derfinder'	advancedArg derfinder-deprecated
Change naming style for a set of sequence names	extendedMapSeqlevels
Filter the positions of interest	filterData
Find non-zero regions in a Rle	findRegions
Load the unfiltered coverage information from a group of BAM files and a list of chromosomes	fullCoverage
Genome samples processed data	genomeData
Genome samples processed data	genomeDataRaw
F-statistics for the example data	genomeFstats
Genome samples information	genomeInfo
Candidate DERs for example data	genomeRegions
Genomic State for Hsapiens.UCSC.hg19.knownGene	genomicState
Extract coverage information for a set of regions	getRegionCoverage
Calculate the total number of mapped reads	getTotalMapped
Load the coverage information from a group of BAM files	loadCoverage
Obtain the genomic state per region from annotation	makeGenomicState
Build model matrices for differential expression	makeModels
Merge results from different chromosomes	mergeResults
Transform and split the data	preprocessCoverage
Identify regions data by a coverage filter and get a count matrix from BigWig files	railMatrix
Construct full paths to a group of raw input files	rawFiles
Identify regions data by a coverage filter and get a count matrix	regionMatrix
Calculate adjustments for library size	sampleDepth

Package: derfinder 1.39.0

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

derfinder quick start guide

derfinder users guide

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)