CDSeq                   Complete deconvolution using sequencing data.
CDSeq-R-package         CDSeq: A package for complete deconvolution
                        using sequencing data
cdseq.result            Output of synthetic mixtures of PBMC scRNAseq
                        data
Cell2RNA                Cell proportion to RNA proportion 'Cell2RNA'
                        converts Cell proportion to RNA proportion
cellTypeAssignSCRNA     'cellTypeAssignSCRNA' assigns CDSeq-identified
                        cell types using single cell RNAseq data.
gene_length             Gene length
gene2rpkm               gene2rpkm outputs the rpkm normalizations of
                        the CDSeq-estimated GEPs. 'gene2rpkm' outputs
                        the rpkm normalizations of the CDSeq-estimated
                        GEPs.
gibbsSampler            This is the Gibbs sampler for CDSeq.
                        'GibbsSampler' returns estimated GEPs and cell
                        type proportions.
hungarian_Rcpp          This is the Hungarian algorithm wrapper for
                        cell type assignment 'hungarian_Rcpp' returns
                        cell type assignment given reference GEPs
intersection            'intersection' take intersection of multiple
                        lists and return the common set and index
logpost                 logpost computes the log posterior of the CDSeq
                        model. 'logpost' outputs the value of log
                        posterior.
max_rep                 'max_rep' Find the element that repeats the
                        most in a given vector and calculate its
                        proportion.
merge_df                Data frame for keeping the CDSeq-estimated cell
                        type proportions for PBMC mixtures
mixtureGEP              Synthetic bulk RNA-seq read counts data of six
                        cell types
pbmc_ggplot             ggplot figures of comparison between
                        CDSeq-estimated cell type proportion and ground
                        truth
pbmc_mix                Synthetic bulk RNA-seq read counts data of PBMC
                        single cell data
read2gene               read2gene outputs the GEP normalized by gene
                        length of the CDSeq-estimated GEPs. 'read2gene'
                        outputs the gene length normalized
                        CDSeq-estimated GEP.
refGEP                  GEPs of six component pure cell lines
result1                 CDSeq result of synthetic bulk RNA-seq read
                        counts data of six cell types
result2                 CDSeq result of synthetic bulk RNA-seq read
                        counts data of six cell types
result3                 CDSeq result of synthetic bulk RNA-seq read
                        counts data of six cell types
RNA2Cell                RNA proportion to cell proportion 'RNA2Cell'
                        converts RNA proportion to cell proportion
sc_annotation           Cell type annotation of the PBMC single cell
                        data
sc_gep                  PBMC single cell RNAseq read counts that used
                        for creating synthetic PBMC mixtures
seedMT                  This is the Mersenne Twister random number
                        generator. 'cokus' generates pseudorandom
                        integers uniformly distributed in 0..(2^32 -
                        1).
SyntheticMixtureData    Synthetic bulk RNA-seq read counts data of six
                        cell types, PBMC mixtures using scRNASeq and
                        some preliminary results
true_GEP_gene           True GEPs of the six component cell types
                        normalized by gene length
true_GEP_read           True GEPs of the six component cell types
                        unnormalized by gene length
true_GEP_rpkm           True GEPs of the six component cell types RPKM
                        normalization
true_prop               True cell type proportion in the PBMC synthetic
                        mixtures
true_prop_cell          True cell proportions of the mixtures
true_prop_RNA           True cell type RNA proportions
