Man pages for AnnikaGable/chromium
Analyze and visualize high throughput chromatin interaction data, such as Hi-C or ChIA-PET
| bin_chrom | Bin an existing InteractionSet |
| chr2 | Hi-C interaction data for chromosome 2 of mouse stem cells |
| Create_any_resolution_LFM | Create a ligation frequency matrix or InteractionSet binned... |
| easy_Iset_to_LFM | Convert an InteractionSet into a sparse, upper triangle... |
| import_chrom | Read preprocessed genomic interaction files into an... |
| IPF_alg | Iterative proportional fitting algorithm |
| Iset_region_to_LFM | Convert an InteractionSet region into a ligation frequency... |
| Iset_to_LFM | Convert an InteractionSet object into a ligation frequency... |
| LFM_to_Iset | Convert a sparse ligation frequency matrix into an... |
| loss_function | Loss function |
| normalize_chrom | Normalize an InteractionSet with iterative proportional... |
| normalize_LFM_iteratively | Normalize a ligation frequency matrix with iterative... |
| pairID_to_RFpair | Decode the pair ID into the bin pairs or restriction fragment... |
| plot_qa | Output a quality assessment report. |
| quality_assessment | Quality assessment of whole genome Hi-C data. |
| read_bed_raf | Read preprocessed genomic interaction files to produce RFanno... |
| RFpairs_to_Iset | Convert restriction fragment annotation and restriction... |
| RFpair_to_pairID | Encode a restriction fragment pair or bin pair into one... |
| rotated_image | Plot a rotated and, if required, smoothed interaction matrix. |
| subset_chrom | Choose a chromosome and a region within which InteractionSet... |
| subset_interactions | Choose a chromosome and a range within which InteractionSet... |
| sym_to_triangle | Convert a sparse symmetric matrix to a sparse triangle... |
| triangle_to_sym | Convert a sparse triangle matrix to a sparse symmetric... |
| visualize_chrom | Triangle visualization of Hi-C data with tracks for chipseq,... |
