Man pages for rosedu1/deconvSeq
Cell Type Deconvolution for RNA Sequencing and Bisulfite Sequencing
| b0 | Projection matrix (RNAseq) |
| b0.sc | projection matrix (scRNAseq) |
| cbc.rnaseq | Known cell type mixture for tissue (RNAseq) |
| cbc.rrbs | Known cell type mixture for tissue (bisulfite sequencing) |
| celltypes.rrbs | vector of kinds of cell types (bisulfite sequencing) |
| cnts.celltypes | Count matrix for cell types (RNAseq) |
| cnts.sc | count matrix for filtered scRNAseq dataset |
| cnts.sc.G1 | count matrix for filtered scRNAseq dataset for cell phase... |
| cnts.scrnaseq | Count matrix for single cell RNAseq (scRNAseq) |
| cnts.tissue | Count matrix for tissue (RNAseq) |
| data_celltypes_rnaseq | This is the example cell type data for RNA sequencing |
| data_celltypes_rrbs | This is the example cell type data for bisulfite sequencing |
| data_scrnaseq | This is the example data for scRNA sequencing |
| data_tissue_rnaseq | This is the example tissue data for RNA sequencing |
| data_tissue_rrbs | This is the example tissue data for bisulfite sequencing |
| design.rnaseq | Design matrix for cell types (RNAseq) |
| design.rrbs | Design matrix for cell types (bisulfite sequencing) |
| design_s.sc | Design matrix (scRNAseq) |
| dge.celltypes | DGE object (from EdgeR) of RNAseq results for cell types |
| dge.sc | DGE for training set (scRNAseq) |
| dge.tissue | DGE object (from EdgeR) of RNAseq results for tissue |
| getb0.biseq | compute b0, projection matrix, given methylation counts |
| getb0.rnaseq | compute b0, projection matrix, given counts |
| getcellcycle | Cell cycle filter |
| getcorr | compute correlation between estimated and actual composition... |
| getdge | Obtain EdgeR DGE object from count matrix |
| getmeancorr | Mean Correlation |
| getmethmat | Makes methylation count matrix |
| getrnamat | Combine count matrix for individual samples |
| getx1.biseq | compute mixture data given projection matrix (bisulfite... |
| getx1.rnaseq | compute mixture data given projection matrix (RNAseq) |
| methmat | methylation matrix for cell types (bisulfite sequencing) |
| methmat.tissue | methylation matrix for tissue (bisulfite sequencing) |
| my_diffMethFromDesign_matrix | modified from methylKit, performs regression given... |
| prep_scrnaseq | Quality control of scRNAseq |
| resultx1 | Results from celltype analysis (RNAseq) |
| resultx1.rrbs | Results from celltypes analysis (bisulfite sequencing) |
| resultx1_s.sc | Results (scRNAseq) |
| resultx1.tissue | Results from tissue analysis (RNAseq) |
| resultx1.tissue.rrbs | Results from tissue analysis (bisulfite sequencing) |
| sample.id.rnaseq | Sample IDs for cell types (RNAseq) |
| sample.id.rrbs | Sample IDs for cell types (bisulfite sequencing) |
| sample.id_s.sc | sample IDs (scRNAseq) |
| sample.id.tissue.rrbs | Sample IDs for tissue (bisulfite sequencing) |
