Package: IntEREst 1.31.0

Ali Oghabian

IntEREst: Intron-Exon Retention Estimator

This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).

Authors:Ali Oghabian <[email protected]>, Dario Greco <[email protected]>, Mikko Frilander <[email protected]>

IntEREst_1.31.0.tar.gz
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IntEREst.pdf |IntEREst.html✨
IntEREst/json (API)
NEWS

# Install 'IntEREst' in R:

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

Datasets:

mdsChr22ExObj - Object of SummarizedExperiment type for exon-exon junction of MDS data
mdsChr22IntSpObj - Object of SummarizedExperiment type for intron spanning reads of MDS data
mdsChr22Obj - Object of SummarizedExperiment type for intron retention MDS data
pwmU12db - PWM of U12 and U2-type introns splice sites
u12 - U12 data

On BioConductor:IntEREst-1.31.0(bioc 3.21)IntEREst-1.30.0(bioc 3.20)

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

software alternativesplicing coverage differentialsplicing sequencing rnaseq alignment normalization differentialexpression immunooncology

3.98 score 12 scripts 238 downloads 2 mentions 35 exports 132 dependencies

Last updated 2 months agofrom:99f637733c. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Dec 10 2024
R-4.5-win	NOTE	Dec 10 2024
R-4.5-linux	NOTE	Dec 10 2024
R-4.4-win	NOTE	Dec 10 2024
R-4.4-mac	NOTE	Dec 10 2024
R-4.3-win	NOTE	Dec 10 2024
R-4.3-mac	NOTE	Dec 10 2024

Exports:addAnnotation annotateU12 applyOverlap buildSsTypePwms counts counts.InterestResults deseqInterest DEXSeqIntEREst exactTestInterest getAnnotation getRepeatTable glmInterest interest interest.sequential InterestResult interestResultIntEx intexBoxplot intexIndex lfc mergeInterestResult psi qlfInterest readInterestResults referencePrepare scaledRetention subInterestResult treatInterest u12Boxplot u12BoxplotNb u12DensityPlot u12DensityPlotIntron u12Index u12NbIndex unionRefTr updateRowDataCol

Dependencies:abind ade4 annotate AnnotationDbi askpass BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings bit bit64 bitops blob BSgenome cachem cli codetools colorspace cpp11 crayon curl DBI dbplyr DelayedArray DESeq2 DEXSeq digest dplyr edgeR fansi farver fastmap filelock formatR futile.logger futile.options genefilter geneplotter generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicFiles GenomicRanges ggplot2 glue gtable hms httr httr2 hwriter IRanges isoband jsonlite KEGGREST labeling lambda.r lattice lifecycle limma locfit lubridate magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme openssl pillar pixmap pkgconfig plogr png prettyunits progress purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RCurl restfulr Rhtslib rjson rlang RMariaDB Rsamtools RSQLite rtracklayer S4Arrays S4Vectors scales segmented seqinr seqLogo snow sp SparseArray statmod stringi stringr SummarizedExperiment survival sys tibble tidyr tidyselect timechange txdbmaker UCSC.utils utf8 VariantAnnotation vctrs viridisLite withr XML xml2 xtable XVector yaml zlibbioc

IntEREst

Ali Oghabian

Rendered fromIntEREst.Rmdusingknitr::rmarkdownon Dec 10 2024.

Last update: 2023-01-03
Started: 2016-12-15

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
IntEREst	IntEREst-package IntEREst
Adding sample annotations to a 'SummarizedExperiment' object	addAnnotation
Annotate the U12 (and U2) type introns	annotateU12
Apply function over counts	applyOverlap
Extracting values of useful attributes of SummarizedExperiment objects	attributes getAnnotation scaledRetention
boxplot - method	boxplot,SummarizedExperiment-method boxplot-method intexBoxplot
Building Position Weight Matrices for Splice Sites of U12 and U2 type introns.	buildSsTypePwms
Counts - method	counts,SummarizedExperiment-method counts-method counts.InterestResults
DESeq2 analysis for IntEREst object	deseqInterest
DEXSeq test for IntEREst object	DEXSeqIntEREst
Exact test	exactTestInterest
Get table of regions with repetetive DNA sequences	getRepeatTable
generalized linear model likelihood ratio tests	glmInterest
Wrapper function: Parallel run	interest
Wrapup function: Sequential running	interest.sequential
Building SummarizedExperiment object from results in IntEREst.	InterestResult
Building results object that contains Intron-retention and exon-exon junction information	interestResultIntEx
Extract index of intron or exon rows	intexIndex
Log fold change	lfc
Object of SummarizedExperiment type for exon-exon junction of MDS data	mdsChr22ExObj
Object of SummarizedExperiment type for intron spanning reads of MDS data	mdsChr22IntSpObj
Object of SummarizedExperiment type for intron retention MDS data	mdsChr22Obj
merge two SummarizedExperiment objects into one	mergeInterestResult
plot - method	plot,SummarizedExperiment,ANY-method plot-method plot.InterestResult
Psi values estimation	psi
PWM of U12 and U2-type introns splice sites	pwmU12db
quasi-likelihood F-test	qlfInterest
Read interest/interest.sequential results text files	readInterestResults
Creates reference file	referencePrepare
Extract subset of object	subInterestResult
Differential retention test relative to a threshold	treatInterest
U12 data	u12
U12 boxplot	u12Boxplot
boxplot U12 introns retention levels (or flanking exons junction levels) and (up/down)stream U2 introns (or exons junction levels)	u12BoxplotNb
Density plot of fld changes of intron retention and exon-exon junction levels	u12DensityPlot u12DensityPlotIntron
Extract index of U12 introns rows	u12Index
Extract index of U2 introns (up/down)stream of U12 introns rows	u12NbIndex
Union introns/exons of transcripts	unionRefTr
Updating contents of 'rowData' of 'SummarizedExperiment' objects	updateRowDataCol