Man pages for neurogenomics/CHAS
Cell type deconvolution of bulk tissue histone acetylomes from epigenetic data
| astro_H3K27ac_hg19 | Astrocyte H3K27ac peaks with hg19 coordinates. |
| astro_H3K27ac_hg38 | Astrocyte H3K27ac peaks with hg38 coordinates. |
| calculate_cpm | Calculate cpm |
| calculate_median_and_variability | Calculate Median and variability |
| CelltypeProportion | Calculate cell type proportions |
| CelltypeScore | Generate cell-type-specific histone acetylation scores |
| CelltypeSpecificPeaks | Identify cell type-specific peaks in bulk tissue H3K27ac... |
| ConsensusPeaks | Find Consensus Peaks |
| EntorhinalCortex_AD_H3K27ac_counts | Entorhinal cortex H3K27ac read counts. |
| EntorhinalCortex_AD_H3K27ac_peaks | Entorhinal cortex H3K27ac peaks with hg38 coordinates. |
| mgl_H3K27ac_hg19 | Microglia H3K27ac peaks with hg19 coordinates. |
| mgl_H3K27ac_hg38 | Microglia H3K27ac peaks with hg38 coordinates. |
| neu_H3K27ac_hg19 | Neuronal H3K27ac peaks with hg19 coordinates. |
| neu_H3K27ac_hg38 | Neuronal H3K27ac peaks with hg38 coordinates. |
| olig_H3K27ac_hg19 | Oligodendrocyte H3K27ac peaks with hg19 coordinates. |
| olig_H3K27ac_hg38 | Oligodendrocyte H3K27ac peaks with hg38 coordinates. |
| plot_celltype_annotations | Plot the proportions of peaks annotated to each cell type |
| plot_celltype_scores | Plot cell type scores between groups |
| plot_correlation | Plot the correlation |
| plot_MF_groups | Plot MF-predicted proportions between groups |
| plot_MF_props | Plot matrix-factorisation-predicted cell type proportions in... |
| ReadCounting | Read Counting |
| ref_H3K27ac_counts_hg19 | Reference H3K27ac read counts. |
| ref_H3K27ac_counts_hg38 | Reference H3K27ac read counts. |
| ref_H3K27ac_peaks_hg19 | Reference H3K27ac peaks with hg19 coordinates. |
| ref_H3K27ac_peaks_hg38 | Reference H3K27ac peaks with hg38 coordinates. |
| run_mf | Run Matrix Factorisation |
| select_signature_peaks | Select Signature Peaks |
| UnionPeaks | Find Union Peaks |
