Package: IMAS 1.31.0
Seonggyun Han
IMAS: Integrative analysis of Multi-omics data for Alternative Splicing
Integrative analysis of Multi-omics data for Alternative splicing.
Authors:
IMAS_1.31.0.tar.gz
IMAS_1.31.0.zip(r-4.5)IMAS_1.31.0.zip(r-4.4)IMAS_1.31.0.zip(r-4.3)
IMAS_1.31.0.tgz(r-4.4-any)IMAS_1.31.0.tgz(r-4.3-any)
IMAS_1.31.0.tar.gz(r-4.5-noble)IMAS_1.31.0.tar.gz(r-4.4-noble)
IMAS_1.31.0.tgz(r-4.4-emscripten)IMAS_1.31.0.tgz(r-4.3-emscripten)
IMAS.pdf |IMAS.html✨
IMAS/json (API)
NEWS
| # Install 'IMAS' in R: |
| install.packages('IMAS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- Clinical.data - A data frame for clinical data
- GroupSam - Group of each sample.
- sampleMedata - Methylation level data
- sampleMelocus - Genomic locus of methylations
- samplebamfiles - A data frame for example expression bam files.
- samplesnp - Genotype data
- samplesnplocus - Genomic locus of SNPs
On BioConductor:IMAS-1.31.0(bioc 3.21)IMAS-1.30.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologyalternativesplicingdifferentialexpressiondifferentialsplicinggeneexpressiongeneregulationregressionrnaseqsequencingsnpsoftwaretranscription
Last updated 2 months agofrom:807fef2843. Checks:OK: 5 NOTE: 2. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | OK | Nov 29 2024 |
| R-4.4-mac | OK | Nov 29 2024 |
| R-4.3-win | OK | Nov 29 2024 |
| R-4.3-mac | OK | Nov 29 2024 |
Exports:ASvisualizationClinicAnalysisCompGroupAltExonsClusterMEsQTLFinderRatioFromReadsSplicingReads
Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobbootcachemclicodetoolscolorspacecpp11crayoncurlDBIDelayedArraydoParalleldplyrfansifarverfastmapforeachformatRfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDataGenomicAlignmentsGenomicFeaturesGenomicRangesggfortifyggplot2gluegridExtragtablehttrIRangesisobanditeratorsIVASjsonliteKEGGRESTlabelinglambda.rlatticelifecyclelme4magrittrMASSMatrixMatrixGenericsmatrixStatsmemoisemgcvmimeminqamunsellnlmenloptropensslpillarpkgconfigplogrpngpurrrR6RColorBrewerRcppRcppEigenRCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsscalessnowSparseArraystringistringrSummarizedExperimentsurvivalsystibbletidyrtidyselectUCSC.utilsutf8vctrsviridisLitewithrXMLXVectoryamlzlibbioc
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 |