Man pages for jwyang16/DECODER
DECODER: DECOnvolution of DNA accEssibility using anchor-based Regression
| bed2granges | transfer bed file to Granges |
| bulk.normalize | Normalize the bulk sample using anchors |
| count2cpm | Transfer raw count matrix to count-per-million (CPM) |
| DECODER | DECODER: Deconvolution of DNA accessibility based on... |
| DECODER.pipeline | DECODER pipeline |
| DECODER.user | Construct cell type-specific reference when ref==user |
| demo | Demo datasets including: bulk.sample: demo bulk ATAC-seq... |
| evaluate | Evaluate the result |
| genomes | Genome reference assembly including: hg19 (200bp per bin),... |
| getcount | get count matrix from peak file and bam files |
| mpredict | Predict using the monotonous smooth spline |
| mspline | Fit monotonous smooth spline |
| peakcalling | do peak calling |
| reference | Cell type-specific references including: human hematopoietic... |
| ref_peak | Peak regions for built-in reference including: human... |
| select.anchor | Select constant anchor loci from single-cell ATAC-seq... |
| select.variable | Select highly variable loci from single-cell ATAC-seq... |
