Package: GeneStructureTools 1.25.0

Beth Signal

GeneStructureTools: Tools for spliced gene structure manipulation and analysis

GeneStructureTools can be used to create in silico alternative splicing events, and analyse potential effects this has on functional gene products.

Authors:Beth Signal

GeneStructureTools_1.25.0.tar.gz
GeneStructureTools_1.25.0.zip(r-4.5)GeneStructureTools_1.25.0.zip(r-4.4)GeneStructureTools_1.25.0.zip(r-4.3)
GeneStructureTools_1.25.0.tgz(r-4.4-any)GeneStructureTools_1.25.0.tgz(r-4.3-any)
GeneStructureTools_1.25.0.tar.gz(r-4.5-noble)GeneStructureTools_1.25.0.tar.gz(r-4.4-noble)
GeneStructureTools_1.25.0.tgz(r-4.4-emscripten)GeneStructureTools_1.25.0.tgz(r-4.3-emscripten)
GeneStructureTools.pdf |GeneStructureTools.html✨
GeneStructureTools/json (API)
NEWS

# Install 'GeneStructureTools' in R:

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

On BioConductor:GeneStructureTools-1.25.0(bioc 3.20)GeneStructureTools-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

40 exports 0.61 score 150 dependencies

Last updated 2 months agofrom:59cccd6ccc

Exports:addBroadTypes addIntronInTranscript alternativeIntronUsage annotateGeneModel attrChangeAltSpliced coordinates DEXSeqIdsToGeneIds diffSplicingResults exonsToTranscripts filterGtfOverlap filterWhippetEvents findDEXexonType findExonContainingTranscripts findIntronContainingTranscripts findJunctionPairs formatWhippetEvents getOrfs getUOrfs junctions leafcutterTranscriptChangeSummary makeGeneModel maxLocation orfDiff orfSimilarity overlapTypes readCounts readWhippetDataSet readWhippetDIFFfiles readWhippetJNCfiles readWhippetPSIfiles removeDuplicateTranscripts removeSameExon removeVersion reorderExonNumbers replaceJunction skipExonInTranscript summariseExonTypes transcriptChangeSummary UTR2UTR53 whippetTranscriptChangeSummary

Dependencies:abind AnnotationDbi AnnotationFilter askpass backports base64enc BH Biobase BiocFileCache BiocGenerics BiocIO BiocParallel biomaRt Biostrings biovizBase bit bit64 bitops blob BSgenome BSgenome.Mmusculus.UCSC.mm10 bslib cachem checkmate cli cluster codetools colorspace cpp11 crayon curl data.table DBI dbplyr DelayedArray deldir dichromat digest dplyr ensembldb evaluate fansi farver fastmap filelock fontawesome foreign formatR Formula fs futile.logger futile.options generics GenomeInfoDb GenomeInfoDbData GenomicAlignments GenomicFeatures GenomicRanges ggplot2 glue gridExtra gtable Gviz highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 interp IRanges isoband jpeg jquerylib jsonlite KEGGREST knitr labeling lambda.r lattice latticeExtra lazyeval lifecycle magrittr MASS Matrix MatrixGenerics matrixStats memoise mgcv mime munsell nlme nnet openssl pillar pkgconfig plogr plyr png prettyunits progress ProtGenerics purrr R6 rappdirs RColorBrewer Rcpp RcppEigen RCurl restfulr Rhtslib rjson rlang rmarkdown rpart Rsamtools RSQLite rstudioapi rtracklayer S4Arrays S4Vectors sass scales snow SparseArray stringdist stringi stringr SummarizedExperiment sys tibble tidyr tidyselect tinytex UCSC.utils utf8 VariantAnnotation vctrs viridis viridisLite withr xfun XML xml2 XVector yaml zlibbioc

Introduction to GeneStructureTools

Beth Signal

Rendered fromVignette.Rmdusingknitr::rmarkdownon Jun 14 2024.

Last update: 2018-03-12
Started: 2018-01-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Change transcript biotypes to a broader set	addBroadTypes
Add a retained intron to the transcripts it is skipped by	addIntronInTranscript
Create transcripts with alternative intron usage	alternativeIntronUsage
Annotate a GRanges gene model with ORF boundries for visualisation with Gviz	annotateGeneModel
Evaluate the change in an attribute between a set of 'normal' transcripts and 'alternative' transcripts	attrChangeAltSpliced
Method coordinates	coordinates coordinates,whippetDataSet-method
Convert DEXSeq ids to gene ids	DEXSeqIdsToGeneIds
Method diffSplicingResults	diffSplicingResults diffSplicingResults,whippetDataSet-method
Convert an exon-level gtf annotation to a transcript-level gtf annotation	exonsToTranscripts
Filter a GTF overlap to remove exons when exon is annotated as a CDS/UTR	filterGtfOverlap
Filter out significant events from a whippet diff comparison	filterWhippetEvents
Find a DEXSeq exons' biotype	findDEXexonType
Given the location of a whole spliced in exon, find transcripts which can splice out this exon	findExonContainingTranscripts
Given the location of a whole retained intron, find transcripts which splice out this intron	findIntronContainingTranscripts
Find alternative junctions for Whippet alternative splicing events	findJunctionPairs
Format Whippet co-ordinates as a GRanges object	formatWhippetEvents
Get open reading frames for transcripts	getOrfs
Get upstream open reading frames for transcripts with annotated main ORFs	getUOrfs
Method junctions	junctions junctions,whippetDataSet-method
Compare open reading frames for whippet differentially spliced events	leafcutterTranscriptChangeSummary
Convert GRanges gene model to data.frame for visualisation with Gviz	makeGeneModel
Find the largest distance between two vectors of numbers Helper function for get_orfs	maxLocation
Evaluate changes to ORFs caused by alternative splicing	orfDiff
calculate percentage of orfB contained in orfA	orfSimilarity
Annotate introns and exonic parts by overlaping exon biotype	overlapTypes
Method readCounts	readCounts readCounts,whippetDataSet-method
Import whippet results files as a whippetDataSet	readWhippetDataSet
Read in a list of whippet .diff.gz files and format as a data.frame	readWhippetDIFFfiles
Read in a list of whippet .jnc.gz files and format as a GRanges object	readWhippetJNCfiles
Read in a list of whippet .psi.gz files and format as a data.frame	readWhippetPSIfiles
Remove transcript duplicates	removeDuplicateTranscripts
Remove exon duplicates	removeSameExon
Remove version number from ensembl gene/transcript ids	removeVersion
Reorder the exon numbers in a gtf annotation	reorderExonNumbers
Find transcripts containing/overlapping junctions and replace them with alternative junctions	replaceJunction
Remove and include a skipped exon from the transcripts it overlaps	skipExonInTranscript
Summarise exon biotypes to broader categories	summariseExonTypes
Compare open reading frames for two sets of paired transcripts	transcriptChangeSummary
Annotate UTRs from Gencode GTF as 5' or 3'	UTR2UTR53
Class whippetDataSet	whippetDataSet-class
Compare open reading frames for whippet differentially spliced events	whippetTranscriptChangeSummary