Changes in version 0.99.0                        

First release prepared for Bioconductor submission. The package was
rewritten from the ground up; nothing of the 0.1.0 prototype other than
the name and the intent remains.

New container

  - OncoSeqExperiment, an S4 class extending SummarizedExperiment, holds
    expression, somatic mutations, gene-level copy number, clinical
    follow-up, an analysis registry and a provenance log for one cohort.
    Validity checking keeps sample identifiers concordant across layers
    and subsetting propagates to every layer.

New data import

  - importGDC() retrieves a TCGA project through TCGAbiolinks. It
    requests the current "STAR - Counts" workflow; the prototype's
    "HTSeq - Counts" request was retired by the GDC at Data Release 32
    and no longer returns data.
  - importCBioPortal(), cbioStudies() and cbioProfiles() query the
    cBioPortal REST API for curated studies.
  - importCounts(), importTximport(), importMAF() and asOncoSeq() cover
    local files and existing objects.

New analysis

  - Quality control: qcMetrics(), filterLowExpression(),
    detectOutliers().
  - Normalisation: normalizeCounts() with CPM, TMM, upper-quartile, RLE,
    VST, rlog and log2-TPM.
  - Differential expression: diffExpress() over DESeq2, edgeR and
    limma-voom behind one contrast interface, plus compareEngines().
  - Enrichment: runGSEA() (fgsea) and runORA() (hypergeometric), with
    readGMT() and msigdbrSets().
  - Genomics: mutationSummary(), mutationFrequency(),
    tumourMutationBurden(), oncoplotData(), cnvSummary(),
    cnvFrequency(), cnvExpressionCorrelation().
  - Survival: survivalFit() with median, tertile, quartile and
    search-corrected optimal cut-points, coxModel() and
    survivalScreen().
  - Integration: mutationStatus(), integrateMutationExpression(),
    alignLayers().
  - Visualisation: nine plot*() functions, all returning ggplot objects.
  - runOncoSeq() chains the central steps in one call.

New data

  - blcaExample, a 420-gene by 400-sample TCGA bladder cancer cohort
    with all four layers, and exampleOncoSeq(), a simulated count-scale
    object for examples and tests.