Package: srnadiff 1.25.0

Zytnicki Matthias

srnadiff: Finding differentially expressed unannotated genomic regions from RNA-seq data

srnadiff is a package that finds differently expressed regions from RNA-seq data at base-resolution level without relying on existing annotation. To do so, the package implements the identify-then-annotate methodology that builds on the idea of combining two pipelines approachs differential expressed regions detection and differential expression quantification. It reads BAM files as input, and outputs a list differentially regions, together with the adjusted p-values.

Authors:Zytnicki Matthias [aut, cre], Gonzalez Ignacio [aut]

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NEWS

# Install 'srnadiff' in R:

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

Uses libs:

c++– GNU Standard C++ Library v3

On BioConductor:srnadiff-1.25.0(bioc 3.20)srnadiff-1.24.0(bioc 3.19)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

bioconductor-package

19 exports 1.08 score 202 dependencies 1 mentions

Last updated 2 months agofrom:7519e6e266

Exports:annotReg annotReg<-bamFiles chromosomeSizes countMatrix coverages normFactors normFactors<-parameters parameters<-plotRegions readAnnotation regions sampleInfo show srnadiff srnadiffDefaultParameters srnadiffExample srnadiffExp

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocManager BiocParallel BiocStyle biomaRt Biostrings biovizBase bit bit64 bitops blob bookdown brew brio BSgenome bslib cachem callr checkmate cli clipr cluster codetools colorspace commonmark cpp11 crayon credentials curl data.table DBI dbplyr DelayedArray deldir desc DESeq2 devtools dichromat diffobj digest downlit dplyr edgeR ellipsis ensembldb evaluate fansi farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges gert ggplot2 gh gitcreds glue gridExtra gtable Gviz highr Hmisc hms htmlTable htmltools htmlwidgets httpuv httr httr2 ini interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r later lattice latticeExtra lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime miniUI munsell nlme nnet openssl pillar pkgbuild pkgconfig pkgdown pkgload plogr png praise prettyunits processx profvis progress promises ProtGenerics ps purrr R6 ragg rappdirs rcmdcheck RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl rematch2 remotes restfulr Rhtslib rjson rlang rmarkdown roxygen2 rpart rprojroot Rsamtools RSQLite rstudioapi rtracklayer rversions S4Arrays S4Vectors sass scales sessioninfo shiny snow sourcetools SparseArray statmod stringi stringr SummarizedExperiment sys systemfonts testthat textshaping tibble tidyr tidyselect tinytex UCSC.utils urlchecker usethis utf8 VariantAnnotation vctrs viridis viridisLite waldo whisker withr xfun XML xml2 xopen xtable XVector yaml zip zlibbioc

"Finding differentially expressed unannotated genomic regions from RNA-seq data with srnadiff"

Matthias Zytnicki, Ignacio González

Rendered fromsrnadiff.Rmdusingknitr::rmarkdownon Jun 14 2024.

Last update: 2023-12-11
Started: 2017-02-22

Help page	Topics
Accessors for the 'annotReg' slot of an srnadiffExp object	annotReg annotReg,srnadiffExp-method annotReg<- annotReg<-,srnadiffExp-method
Accessors for the 'bamFiles' slot of an srnadiffExp object	bamFiles bamFiles,srnadiffExp-method
Accessors for the 'chromosomeSizes' slot of an srnadiffExp object	chromosomeSizes chromosomeSizes,srnadiffExp-method
Accessors for the 'countMatrix' slot of an srnadiffExp object	countMatrix countMatrix,srnadiffExp-method
Accessors for the 'coverages' slot of an srnadiffExp object	coverages coverages,srnadiffExp-method
Accessors for the 'normFactors' slot of an srnadiffExp object	normFactors normFactors,srnadiffExp-method normFactors<- normFactors<-,srnadiffExp,numeric-method
Accessors for the 'parameters' slot of an srnadiffExp object	parameters parameters,srnadiffExp-method parameters<- parameters<-,srnadiffExp-method print.srnadiff_par
Plot the coverage information surrounding genomic regions	plotRegions
Reads and parses GFF/GTF files	readAnnotation
Extracts differentially expressed regions of an srnadiffExp object	regions regions,srnadiffExp-method
Accessors for the 'sampleInfo' slot of an srnadiffExp object	sampleInfo sampleInfo,srnadiffExp-method
Finding differentially expressed unannotated genomic regions from RNA-seq data	srnadiff-package srnadiff
List of srnadiff default parameters.	srnadiffDefaultParameters
Example constructor	srnadiffExample
Infrastructure for sRNA-Seq experiment and differential expression	show,srnadiffExp-method srnadiffExp srnadiffExp-class

Package: srnadiff 1.25.0

srnadiff: Finding differentially expressed unannotated genomic regions from RNA-seq data

"Finding differentially expressed unannotated genomic regions from RNA-seq data with srnadiff"

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