Package: splicelogic 1.1.2

Beatriz Campillo

splicelogic: splicelogic: differential transcripts to splice events

Translate differential transcript usage results into discrete splice events.

Authors:Beatriz Campillo [aut, cre], Michael Love [aut], NIH NHGRI [fnd], Wellcome Trust [fnd]

splicelogic_1.1.2.tar.gz
splicelogic_1.1.2.zip(r-4.7)splicelogic_1.1.2.zip(r-4.6)splicelogic_1.1.2.zip(r-4.5)
splicelogic_1.1.2.tgz(r-4.6-any)splicelogic_1.1.2.tgz(r-4.5-any)
splicelogic_1.1.2.tar.gz(r-4.7-any)splicelogic_1.1.2.tar.gz(r-4.6-any)
splicelogic_1.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
splicelogic/json (API)

# Install 'splicelogic' in R:

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

Bug tracker:https://github.com/thelovelab/splicelogic/issues

Pkgdown/docs site:https://thelovelab.github.io

On BioConductor:splicelogic-1.1.2(bioc 3.24)splicelogic-1.0.1(bioc 3.23)

alternativesplicing differentialsplicing transcriptomics rnaseq longread annotation functionalgenomics dtu splicing

5.52 score 1 stars 2 scripts 139 downloads 16 exports 63 dependencies

Last updated from:c11b5e52fd. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time	Files	Syslog
bioc-checks	NOTE	182
linux-devel-x86_64	OK	296
source / vignettes	OK	470
linux-release-x86_64	OK	268
macos-release-arm64	OK	139
macos-oldrel-arm64	OK	171
windows-devel	OK	195
windows-release	OK	208
windows-oldrel	OK	168
wasm-release	OK	164

Exports:create_mock_data find_a3ss find_a5ss find_all_events find_ie find_mxe find_ri find_se generate_a3ss generate_a5ss generate_mxe generate_ri generate_se prepare_exons prepare_exons_by_partition preprocess

Dependencies:abind askpass BH Biobase BiocBaseUtils BiocGenerics BiocIO BiocParallel Biostrings bitops cigarillo cli codetools cpp11 crayon curl DelayedArray dplyr formatR futile.logger futile.options generics GenomicAlignments GenomicRanges glue httr IRanges jsonlite lambda.r lattice lifecycle magrittr Matrix MatrixGenerics matrixStats mime openssl pillar pkgconfig plyranges R6 RCurl restfulr Rhtslib rjson rlang Rsamtools rtracklayer S4Arrays S4Vectors Seqinfo snow SparseArray SummarizedExperiment sys tibble tidyselect utf8 vctrs withr XML XVector yaml

splicelogic: differential transcripts to splice events

Introduction | Related methods | Quick start | Input data | Output format | Jones et al mouse long read dataset | Loading example data | Finding splicing events | Preprocessing input data | Finding individual events | Finding all events | Upstream methods | Obtaining exon ranges | Using prepare_exons() | Using prepare_exons_by_partition() | Manual construction | Session info

Rendered fromsplicelogic.Rmdusingknitr::rmarkdown

Last update: 2026-05-13
Started: 2026-02-03

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
splicelogic: differential transcripts to splice events	splicelogic-package splicelogic
Create mock GRanges data for splicing event testing	create_mock_data
Find splice events from annotated exons	find_a3ss find_a5ss find_all_events find_events find_ie find_mxe find_ri find_se
Generate mock splice events in a GRanges object	generate_a3ss generate_a5ss generate_events generate_mxe generate_ri generate_se
Prepare exon ranges from a TxDb and DTU results table	prepare_exons
Prepare exons from two transcript partitions	prepare_exons_by_partition
Preprocess input GRanges object for splicing event calculation	preprocess

Usage by other packages (reverse dependencies)