Package: isomiRs 1.41.0

Lorena Pantano

isomiRs: Analyze isomiRs and miRNAs from small RNA-seq

Characterization of miRNAs and isomiRs, clustering and differential expression.

Authors:Lorena Pantano [aut, cre], Georgia Escaramis [aut]

isomiRs_1.41.0.tar.gz
isomiRs_1.41.0.zip(r-4.7)isomiRs_1.41.0.zip(r-4.6)isomiRs_1.41.0.zip(r-4.5)
isomiRs_1.41.0.tgz(r-4.6-any)isomiRs_1.41.0.tgz(r-4.5-any)
isomiRs_1.41.0.tar.gz(r-4.7-any)isomiRs_1.41.0.tar.gz(r-4.6-any)
isomiRs_1.41.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
isomiRs/json (API)

# Install 'isomiRs' in R:

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

Bug tracker:https://github.com/lpantano/isomirs/issues

Datasets:

dat286.long - Data frame containing mirna from Argyropoulos's paper
ego - EnrichResult class
gene_ex_rse - Data frame containing gene expression data
ma_ex - Data frame containing gene-mirna relationship
mirData - Example of IsomirDataSeq with human brain miRNA counts data
mirna_ex_rse - Data frame containing mirna expression data
mirTritation - Data frame containing mirna from Argyropoulos's paper

On BioConductor:isomiRs-1.41.0(bioc 3.24)isomiRs-1.40.0(bioc 3.23)

mirna rnaseq differentialexpression clustering immunooncology analyze-isomirs bioconductor isomirs

7.02 score 8 stars 36 scripts 2 mentions 16 exports 133 dependencies

Last updated from:63a2ae248a. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	229
linux-devel-x86_64	NOTE	501
source / vignettes	OK	691
linux-release-x86_64	NOTE	457
macos-release-arm64	NOTE	221
macos-oldrel-arm64	NOTE	219
windows-devel	NOTE	368
windows-release	NOTE	371
windows-oldrel	NOTE	369
wasm-release	OK	183

Exports:counts counts<-design design<-isoAnnotate isoCounts isoDE IsomirDataSeqFromFiles IsomirDataSeqFromMirtop IsomirDataSeqFromRawData isoNorm isoPlot isoPlotPosition isoSelect isoTop updateIsomirDataSeq

Dependencies:abind ALL AnnotationDbi askpass backports BH Biobase BiocGenerics BiocParallel Biostrings bit bit64 bitops blob broom cachem caTools circlize cli clipr clue cluster codetools colorspace ComplexHeatmap ConsensusClusterPlus cowplot cpp11 crayon curl DBI DEGreport DelayedArray dendextend DESeq2 digest doParallel dplyr edgeR evaluate farver fastmap forcats foreach formatR futile.logger futile.options generics GenomicRanges GetoptLong GGally ggdendro ggplot2 ggrepel ggstats GlobalOptions glue GPArotation gplots gridExtra gtable gtools highr hms httr IRanges isoband iterators jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice lifecycle limma locfit logging magrittr MASS Matrix MatrixGenerics matrixStats memoise mime mnormt nlme openssl patchwork pillar pkgconfig plyr png prettyunits progress psych purrr R6 RColorBrewer Rcpp RcppArmadillo readr reshape rjson rlang RSQLite S4Arrays S4Vectors S7 scales Seqinfo shape snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tzdb utf8 vctrs viridis viridisLite vroom withr xfun XVector yaml

Characterization of miRNA and isomiR molecules

Rendered fromisomiRs.Rmdusingknitr::rmarkdown

Last update: 2025-08-01
Started: 2018-02-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
isomiRs	isomiRs-package isomiRs
Accessors for the count matrix of a IsomirDataSeq object.	counts counts,IsomirDataSeq-method counts.IsomirDataSeq counts<-,IsomirDataSeq,matrix-method
Data frame containing mirna from Argyropoulos's paper	dat286.long
Accessors for the 'design' slot of a IsomirDataSeq object.	design design,IsomirDataSeq-method design<-,IsomirDataSeq,formula-method
enrichResult class	ego
Data frame containing gene expression data	gene_ex_rse
Annotate the rawData of the IsomirDataSeq object	isoAnnotate
Create count matrix with different summarizing options	isoCounts
Differential expression analysis with DESeq2	isoDE
Class that contains all isomiRs annotation for all samples	IsomirDataSeq IsomirDataSeq-class
Loads miRNA annotation from seqbuster tool or pre-processed data.	IsomirDataSeqFromFiles
Import 'mirtop' output into 'IsomirDataSeq'	IsomirDataSeqFromMirtop
Loads miRNA annotation from seqbuster tool or pre-processed data.	IsomirDataSeqFromRawData
Normalize count matrix	isoNorm
Plot the amount of isomiRs in different samples	isoPlot
Plot nucleotides changes at a given position	isoPlotPosition
Method to select specific miRNAs from an IsomirDataSeq object.	isoSelect isoSelect,IsomirDataSeq-method isoSelect.IsomirDataSeq
Heatmap of the top expressed isomiRs	isoTop
Data frame containing gene-mirna relationship	ma_ex
Example of IsomirDataSeq with human brain miRNA counts data	mirData
Data frame containing mirna expression data	mirna_ex_rse
Data frame containing mirna from Argyropoulos's paper	mirTritation
Update IsomirDataSeq object from version < 1.7	updateIsomirDataSeq