Package: diffUTR 1.15.0

Pierre-Luc Germain

diffUTR: diffUTR: Streamlining differential exon and 3' UTR usage

The diffUTR package provides a uniform interface and plotting functions for limma/edgeR/DEXSeq -powered differential bin/exon usage. It includes in addition an improved version of the limma::diffSplice method. Most importantly, diffUTR further extends the application of these frameworks to differential UTR usage analysis using poly-A site databases.

Authors:Pierre-Luc Germain [cre, aut], Stefan Gerber [aut]

diffUTR_1.15.0.tar.gz
diffUTR_1.15.0.zip(r-4.5)diffUTR_1.15.0.zip(r-4.4)diffUTR_1.15.0.zip(r-4.3)
diffUTR_1.15.0.tgz(r-4.4-any)diffUTR_1.15.0.tgz(r-4.3-any)
diffUTR_1.15.0.tar.gz(r-4.5-noble)diffUTR_1.15.0.tar.gz(r-4.4-noble)
diffUTR_1.15.0.tgz(r-4.4-emscripten)diffUTR_1.15.0.tgz(r-4.3-emscripten)
diffUTR.pdf |diffUTR.html✨
diffUTR/json (API)
NEWS

# Install 'diffUTR' in R:

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

Bug tracker:https://github.com/ethz-ins/diffutr/issues

Datasets:

example_bin_se - Example bin-level 'RangedSummarizedExperiment'
example_gene_annotation - Example gene annotation
rn6_PAS - Poly-A sites compendium for Rattus Norvegicus

On BioConductor:diffUTR-1.15.0(bioc 3.21)diffUTR-1.14.0(bioc 3.20)

geneexpression

5.38 score 6 stars 8 scripts 162 downloads 1 mentions 12 exports 135 dependencies

Last updated 23 days agofrom:43fce8477c. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 18 2024
R-4.5-win	WARNING	Nov 18 2024
R-4.5-linux	WARNING	Nov 18 2024
R-4.4-win	WARNING	Nov 18 2024
R-4.4-mac	WARNING	Nov 18 2024
R-4.3-win	WARNING	Nov 18 2024
R-4.3-mac	WARNING	Nov 18 2024

Exports:addNormalizedAssays countFeatures deuBinPlot DEXSeqWrapper diffSplice2 diffSpliceDGEWrapper diffSpliceWrapper geneBinHeatmap geneLevelStats plotTopGenes prepareBins simesAggregation

Dependencies:abind annotate AnnotationDbi AnnotationFilter askpass BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob cachem circlize cli clue cluster codetools colorspace ComplexHeatmap cpp11 crayon curl DBI dbplyr DelayedArray DESeq2 DEXSeq digest doParallel dplyr edgeR ensembldb fansi farver fastmap filelock foreach formatR futile.logger futile.options genefilter geneplotter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges GetoptLong ggplot2 ggrepel GlobalOptions glue gtable hms httr httr2 hwriter IRanges isoband iterators jsonlite KEGGREST labeling lambda.r lattice lazyeval lifecycle limma locfit magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pkgconfig plogr png prettyunits progress ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RCurl restfulr Rhtslib rjson rlang Rsamtools RSQLite Rsubread rtracklayer S4Arrays S4Vectors scales shape snow SparseArray statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect UCSC.utils utf8 vctrs viridisLite withr XML xml2 xtable XVector yaml zlibbioc

diffUTR

Pierre-Luc Germain

Rendered fromdiffUTR.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2021-05-03
Started: 2021-02-04

diffUTR - diffSplice2

Stefan Gerber, Pierre-Luc Germain

Rendered fromdiffSplice2.Rmdusingknitr::rmarkdownon Nov 18 2024.

Last update: 2021-05-03
Started: 2021-05-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
addNormalizedAssays	addNormalizedAssays
countFeatures	countFeatures
deuBinPlot	deuBinPlot
diffSplice2	diffSplice2
DEUwrappers	DEUwrappers DEXSeqWrapper diffSpliceDGEWrapper diffSpliceWrapper
Example bin-level `RangedSummarizedExperiment`	example_bin_se
Example gene annotation	example_gene_annotation
geneBinHeatmap	geneBinHeatmap
geneLevelStats	geneLevelStats
plotTopGenes	plotTopGenes
prepareBins	prepareBins
Poly-A sites compendium for Rattus Norvegicus (Rno6)	rn6_PAS
simesAggregation	simesAggregation