Man pages for cnobles/gintools
Genomic DNA Integration Analysis Tools
| asanmat | An Asymmetric Scaled Ambiguous Nucleotide scoring Matrix... |
| banmat | A Binary Ambiguous Nucleotide scoring Matrix (BAN Mat) |
| break_connecting_source_paths | Break graph paths which connect sources. |
| cluster_kv | Cluster or group key - value(s) pairs |
| cluster_multihits | Identified clusters for multihit integration sites. |
| condense_intsites | Condense integration site GRanges to distinct genomic... |
| connect_adjacent_clusters | Connect adjacent clusters when their sources are within a... |
| connect_satalite_vertices | Connect integration sites which lie a specific gap distance... |
| db_to_granges | Convert an INSPIIRED database query into a GRanges object. |
| determine_abundance | Determine the abundance of integration sites within a GRanges... |
| dot-clusterSites | Cluster/Correct values within a window based on their... |
| dot-standardizeSites | Wrapper around .clusterSites() for standardizing integration... |
| generate_posid | Generate position IDs. |
| generate_test_granges | Generate a test GRanges object |
| graph_clusters | Generate a graph from integrations sites within a specified... |
| normalize_multihit_clusters | Normalize multihit cluster IDs from multiple samples. |
| pop_calcs | Calculation for descriptors of populations |
| refine_breakpoints | Refine or resolve sonic break points within a dataset |
| resolve_cluster_sources | Resolve primary sources from clusters with multiple souce... |
| scan_format | Format a set of GRanges objects for geneRxCluster |
| serial_cluster | Generate clusterIDs for integration sites given multiple gap... |
| sinks | Identify sinks in a directed graph |
| sources | Identify sources in a directed graph |
| ssanmat | A Symmetric Scaled Ambiguous Nucleotide scoring Matrix (SSAN... |
| standardize_sites | Standardize genomic site positions within a dataset |
| track_clones | Identifies or tracks integration sites through multiple... |
| unique_granges | Determine all unique rows in GRanges object |
| vcollapse | Collapse row contents of a data.frame or matrix into single... |
| vintersect | Identify intersection between multiple vectors |
| vzip | Zip vectors together into a single vector. |
| write_demultiplexed_sequences | Write demultiplexed sequences to fasta/q files in an output... |
