Package: splicelogic 1.1.5
Beatriz Campillo
splicelogic: splicelogic: differential transcripts to splice events
Translate differential transcript usage results into discrete splice events.
Authors:
splicelogic_1.1.5.tar.gz
splicelogic_1.1.5.zip(r-4.7-any)splicelogic_1.1.5.zip(r-4.6-any)splicelogic_1.1.5.zip(r-4.5-any)
splicelogic_1.1.5.tgz(r-4.6-any)splicelogic_1.1.5.tgz(r-4.5-any)
splicelogic_1.1.5.tar.gz(r-4.7-any)splicelogic_1.1.5.tar.gz(r-4.6-any)
splicelogic_1.1.5.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-1.1.4(bioc 3.24)splicelogic-1.0.1(bioc 3.23)
alternativesplicingdifferentialsplicingtranscriptomicsrnaseqlongreadannotationfunctionalgenomicsdtusplicing
Last updated from:c25b4e6c28. Checks:1 WARNING, 8 ERROR, 1 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | WARNING | 229 | ||
| linux-devel | ERROR | 529 | ||
| source / vignettes | ERROR | 334 | ||
| linux-release | ERROR | 554 | ||
| macos-release | ERROR | 380 | ||
| macos-oldrel | ERROR | 336 | ||
| windows-devel | ERROR | 572 | ||
| windows-release | ERROR | 417 | ||
| windows-oldrel | ERROR | 380 | ||
| wasm-release | OK | 195 |
Exports:create_mock_dataevent_palettefind_a3ssfind_a5ssfind_all_eventsfind_alternative_3_prime_splice_sitesfind_alternative_5_prime_splice_sitesfind_alternative_transcription_end_sitesfind_alternative_transcription_start_sitesfind_atesfind_atssfind_iefind_included_exonsfind_mutually_exclusive_exonsfind_mxefind_retained_intronsfind_rifind_sefind_sifind_skipped_exonsfind_spliced_intronsgenerate_a3ssgenerate_a5ssgenerate_atesgenerate_atssgenerate_mxegenerate_rigenerate_seget_seqplot_transcript_lfcplot_transcriptsplot_transcripts_by_geneplot_transcripts_by_pairprepare_exonsprepare_exons_by_partitionpreprocess
Dependencies:askpassBHBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitopscigarilloclicodetoolscpp11crayoncurldplyrformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicRangesgluehttrIRangesjsonlitelambda.rlifecyclemagrittrmimeopensslpillarpkgconfigplyrangesR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsrtracklayerS4VectorsSeqinfosnowsystibbletidyselectutf8vctrswithrXMLXVectoryaml
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 |
| Default fill colours for splicelogic event types | event_palette |
| Find splice events from annotated exons | find_a3ss find_a5ss find_all_events find_alternative_3_prime_splice_sites find_alternative_5_prime_splice_sites find_alternative_transcription_end_sites find_alternative_transcription_start_sites find_ates find_atss find_events find_ie find_included_exons find_mutually_exclusive_exons find_mxe find_retained_introns find_ri find_se find_si find_skipped_exons find_spliced_introns |
| Generate mock splice events in a GRanges object | generate_a3ss generate_a5ss generate_ates generate_atss generate_events generate_mxe generate_ri generate_se |
| Extract sequences for GRanges | get_seq |
| Plot a per-transcript fold change for the transcripts of splicelogic events | plot_transcript_lfc |
| Plot the transcripts involved in splicelogic events | plot_transcripts |
| Plot the transcripts involved in splicelogic events, one plot per gene | plot_transcripts_by_gene |
| Plot the transcripts involved in splicelogic events, one plot per pair | plot_transcripts_by_pair |
| 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 |