Package: isomiRs 1.35.0

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_1.35.0.tar.gz
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isomiRs_1.35.0.tgz(r-4.4-any)isomiRs_1.33.2.tgz(r-4.3-any)
isomiRs_1.35.0.tar.gz(r-4.5-noble)isomiRs_1.35.0.tar.gz(r-4.4-noble)
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isomiRs.pdf |isomiRs.html✨
isomiRs/json (API)
NEWS

# 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
mirTritation - Data frame containing mirna from Argyropoulos's paper
mirna_ex_rse - Data frame containing mirna expression data

On BioConductor:isomiRs-1.33.2(bioc 3.20)isomiRs-1.32.1(bioc 3.19)

mirna rnaseq differentialexpression clustering immunooncology analyze-isomirs bioconductor isomirs

7.05 score 8 stars 39 scripts 309 downloads 2 mentions 20 exports 139 dependencies

Last updated 25 days agofrom:b036effbbe. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 30 2024
R-4.5-win	NOTE	Oct 31 2024
R-4.5-linux	NOTE	Oct 30 2024
R-4.4-win	NOTE	Oct 31 2024
R-4.4-mac	NOTE	Oct 31 2024
R-4.3-win	NOTE	Sep 23 2024
R-4.3-mac	NOTE	Sep 23 2024

Exports:counts counts<-design design<-findTargets isoAnnotate isoCounts isoDE IsomirDataSeqFromFiles IsomirDataSeqFromMirtop IsomirDataSeqFromRawData isoNetwork isoNorm isoPlot isoPlotNet isoPlotPosition isoSelect isoTop mirna2targetscan 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 fansi farver fastmap forcats foreach formatR futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData 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 mgcv mime mnormt munsell nlme openssl patchwork pillar pkgconfig plogr plyr png prettyunits progress psych purrr R6 RColorBrewer Rcpp RcppArmadillo readr reshape rjson rlang RSQLite S4Arrays S4Vectors scales shape snow SparseArray statmod stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tzdb UCSC.utils utf8 vctrs viridis viridisLite vroom withr xfun XVector yaml zlibbioc

Characterization of miRNA and isomiR molecules

Lorena Pantano

Rendered fromisomiRs.Rmdusingknitr::rmarkdownon Oct 30 2024.

Last update: 2024-03-13
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
Find miRNAs target using mRNA/miRNA expression	findTargets
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
Clustering miRNAs-genes pairs in similar pattern expression	isoNetwork
Normalize count matrix	isoNorm
Plot the amount of isomiRs in different samples	isoPlot
Functional miRNA / gene expression profile plot	isoPlotNet
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
Find targets in targetscan database	mirna2targetscan
Data frame containing mirna from Argyropoulos's paper	mirTritation
Update IsomirDataSeq object from version < 1.7	updateIsomirDataSeq