Package: isoformic 0.1.2.9017

isoformic: Isoform-Level Biological Interpretation of Transcriptomic Data

Isoform-level biological interpretation of transcriptomic data.

Authors:Lucio Rezende Queiroz [aut, cre, cph], Lucio Rezende Queiroz [aut, ctb], Izabela Mamede Conceicao [aut, ctb], Luigi Marchionni [aut, ctb], Gloria Franco [aut, ctb]

isoformic_0.1.2.9017.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
isoformic/json (API)

# Install 'isoformic' in R:
install.packages('isoformic', repos = c('https://luciorq.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/luciorq/isoformic/issues

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

On CRAN:

Conda:

bioconductorbioinformaticstranscriptomicsquarto

5.48 score 38 stars 10 scripts 36 exports 166 dependencies

Last updated from:c1719472c9. Checks:5 ERROR, 4 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64ERROR347
source / vignettesOK1073
linux-release-x86_64ERROR327
macos-release-arm64OK331
macos-oldrel-arm64OK363
windows-develERROR283
windows-releaseERROR254
windows-oldrelERROR264
wasm-releaseOK293

Exports:annot_dataannot_data_exonsannot_data_genesannot_data_transcriptsannot_row_namesas_isoformiccol_datacol_namesContextDatacreate_context_datade_genede_txdownload_referenceget_isoformic_cacheis_deg_sigIsoformicExperimentjoin_DEG_DETmake_tx_to_geneplot_genomic_contextplot_log2fcplot_log2FCplot_tx_contextplot_tx_exprprepare_annotationprepare_annotation_dbprepare_exon_annotationprepare_isoformic_annotationprepare_profile_datarow_datarow_namesrun_enrichmentsalmon_indexsalmon_quanttx_annottx_to_genetx_type_palette

Dependencies:abindAnnotationDbiarrowaskpassassertthatbackportsBHBiobaseBiocBaseUtilsBiocFileCacheBiocGenericsBiocIObiocmakeBiocParallelbiomaRtBiostringsbitbit64bitopsblobbootbroomcachemcarcarDatacigarilloclicliprcodetoolscolorspacecorrplotcowplotcpp11crayoncurldata.tableDBIdbplyrDelayedArrayDerivdigestdir.expirydoBydplyrduckdbfarverfastmapfilelockforecastformatRFormulafracdifffsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomicAlignmentsGenomicFeaturesGenomicRangesggplot2ggplotifyggpubrggrepelggsciggsignifgluegridExtragridGraphicsgtablehmshttrhttr2IRangesisobandjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelme4lmtestmagrittrMASSMatrixMatrixGenericsMatrixModelsmatrixStatsmemoisemgcvmicrobenchmarkmimeminqamodelrnlmenloptrnnetnumDerivopensslpbkrtestpillarpkgconfigplotgardenerplyrangespngpolynomprettyunitsprogresspurrrquantregR6rappdirsrbibutilsRColorBrewerRcppRcppArmadilloRcppEigenRCurlRdpackreadrreformulasrestfulrrhdf5rhdf5filtersRhdf5libRhtslibrjsonrlangRsamtoolsRSQLiterstatixrtracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraySparseMstrawrstringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselecttimeDatetxdbmakertzdbUCSC.utilsurcautf8vctrsviridisLitevroomwithrXMLxml2XVectoryamlyulab.utilszoo

Preprocessing Sequencing Files
Salmon: command command line interface anatomy | From the Terminal - Salmon Command Line Interface | From R - condathis wrapper for Salmon | Load Data and Create IsoformicExperiment Object | Load Salmon Quantification with tximport
Rendered fromisoformic-preprocess.qmdusingquarto::html

Last update: 2025-11-11
Started: 2025-11-11

Introduction to Isoformic
The Isoformic method | Information | Setting up the data | Initial Considerations | Part 1: Data input | Download reference files | Part 2: Transcript to Gene and Gene to transcript reference tables | Part 3: Constructing the main table | Colors | Log2FC Plot | Profile Plot | Functional Transcript Enrichment | Genomic Context Plot | Protein coding example | Session Information | References
Rendered fromisoformic-table-based.qmdusingquarto::html

Last update: 2025-11-11
Started: 2025-11-11