Package: IMAS 1.36.0
Seonggyun Han
IMAS: Integrative analysis of Multi-omics data for Alternative Splicing
Integrative analysis of Multi-omics data for Alternative splicing.
Authors:
IMAS_1.36.0.tar.gz
IMAS_1.36.0.zip(r-4.7)IMAS_1.36.0.zip(r-4.6)IMAS_1.36.0.zip(r-4.5)
IMAS_1.36.0.tgz(r-4.6-any)IMAS_1.36.0.tgz(r-4.5-any)
IMAS_1.36.0.tar.gz(r-4.7-any)IMAS_1.36.0.tar.gz(r-4.6-any)
IMAS_1.36.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
IMAS/json (API)
NEWS
| # Install 'IMAS' in R: |
| install.packages('IMAS', repos = c('https://bioc-release.r-universe.dev', 'https://cloud.r-project.org')) |
- Clinical.data - A data frame for clinical data
- GroupSam - Group of each sample.
- samplebamfiles - A data frame for example expression bam files.
- sampleMedata - Methylation level data
- sampleMelocus - Genomic locus of methylations
- samplesnp - Genotype data
- samplesnplocus - Genomic locus of SNPs
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologyalternativesplicingdifferentialexpressiondifferentialsplicinggeneexpressiongeneregulationregressionrnaseqsequencingsnpsoftwaretranscription
Last updated from:0c9565fdb4 (on RELEASE_3_23). Checks:2 ERROR, 7 WARNING, 1 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | ERROR | 205 | ||
| linux-devel-x86_64 | WARNING | 474 | ||
| source / vignettes | ERROR | 331 | ||
| linux-release-x86_64 | WARNING | 449 | ||
| macos-release-arm64 | WARNING | 230 | ||
| macos-oldrel-arm64 | WARNING | 251 | ||
| windows-devel | WARNING | 426 | ||
| windows-release | WARNING | 332 | ||
| windows-oldrel | WARNING | 366 | ||
| wasm-release | OK | 161 |
Exports:ASvisualizationClinicAnalysisCompGroupAltExonsClusterMEsQTLFinderRatioFromReadsSplicingReads
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbootcachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArraydoParalleldplyrfarverfastmapforeachformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesggfortifyggplot2gluegridExtragtablehttrIRangesisobanditeratorsIVASjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemimeminqanlmenloptropensslpillarpkgconfigpngpurrrR6rbibutilsRColorBrewerRcppRcppEigenRCurlRdpackreformulasrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsS7scalesSeqinfosnowSparseArraystringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectutf8vctrsviridisLitewithrXMLXVectoryaml
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| 'IMAS': Integrative analysis of Multi-omics data for Alternative Splicing | IMAS-package IMAS |
| Visualize the results of the ASdb object. | ASvisualization |
| A data frame for clinical data | Clinical.data |
| Analysis for differential clinical outcomes across PSI values | ClinicAnalysis |
| Identify alternatively spliced exons with a differential PSIs between the groups | CompGroupAlt |
| Construct representative Exons | ExonsCluster |
| Group of each sample. | GroupSam |
| Identify methylation loci that are significantly associated with alternatively spliced exons | MEsQTLFinder |
| Calculate expression ratio (PSI) from bamfiles | RatioFromReads |
| A data frame for example expression bam files. | samplebamfiles |
| Methylation level data | sampleMedata |
| Genomic locus of methylations | sampleMelocus |
| Genotype data | samplesnp |
| Genomic locus of SNPs | samplesnplocus |
| Count a junction and paired-end reads | SplicingReads |