Biobase, S4Vectors, IRanges, GenomicRanges, Rsamtools,
AnnotationDbi, oligoClasses, oligo, affyPLM, flowClust, affy,
DESeq2, MSnbase, annotate, RUnit

S3-classes-as-S4-classes.R utils.R normarg-utils.R
hotfix73465.R replaceSlots.R append.R as.data.frame.R as.list.R
as.vector.R cbind.R do.call.R duplicated.R eval.R Extremes.R
funprog.R get.R grep.R is.unsorted.R lapply.R mapply.R match.R
matrix-summary.R mean.R nrow.R order.R paste.R rank.R rep.R
row_colnames.R sets.R sort.R start.R subset.R t.R table.R
tapply.R unique.R unlist.R unsplit.R relist.R var.R which.R
boxplot.R image.R density.R IQR.R mad.R residuals.R weights.R
xtabs.R clusterApply.R annotation.R combine.R dbconn.R dge.R
dims.R fileName.R normalize.R Ontology.R organism_species.R
path.R plotMA.R plotPCA.R score.R strand.R toTable.R
updateObject.R testPackage.R zzz.R

Import and summarize transcript-level estimates for transcript-
and gene-level analysis

Imports transcript-level abundance, estimated counts and
        transcript lengths, and summarizes into matrices for use with
        downstream gene-level analysis packages. Average transcript
        length, weighted by sample-specific transcript abundance
        estimates, is provided as a matrix which can be used as an
        offset for different expression of gene-level counts.

Michael Love [cre,aut], Charlotte Soneson [aut], Mark Robinson [aut],
        Rob Patro [ctb], Andrew Parker Morgan [ctb], Ryan C. Thompson [ctb], 
        Matt Shirley [ctb], Avi Srivastava [ctb]

knitr, rmarkdown, testthat, tximportData,
TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), limma,
edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats, Matrix

DataImport, Preprocessing, RNASeq, Transcriptomics,
Transcription, GeneExpression, ImmunoOncology

c(
    person("Alexander", "Walker",
    email = "Alexander.Walker1989@gmail.com", role = c("aut", "cre")),
    person("Luca", "Braglia", role = "ctb"))

Simplifies the creation of Excel .xlsx files by providing a high
    level interface to writing, styling and editing worksheets. Through the use of
    'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect' packages
    with the added benefit of removing the dependency on Java.