Man pages for TmCalculator
Genome-Wide Nucleic Acid Melting Temperature Profiling and Multi-Omics Integration
| cash-.TmCalculator | Lazy '$df' accessor for 'TmCalculator' objects |
| check_filter_seq | Filter invalid bases in nucleotide sequences |
| chem_correct | Corrections of melting temperature with chemical substances |
| compare_groups | Compare numeric GRanges metadata across groups |
| complement_fast | Fast complement and reverse complement |
| coor_to_genomic_ranges | Convert genomic coordinate strings to a GRanges object |
| dot-chem_correct_vec | Vectorized chemical correction over per-sequence GC percent |
| dot-fasta_lengths | Record lengths of a FASTA file, without reading the sequences |
| dot-filter_N_windows | Filter windows with too many N bases |
| dot-find_N_bounds | Detect the first and last non-N positions on a chromosome |
| dot-gc_vec | Vectorized GC percent over a character vector of sequences |
| dot-get_bsgenome_from_pkg | Load the BSgenome object from an installed BSgenome.* data... |
| dot-getseq_preload_chr | Sequence extraction by preloading whole chromosomes |
| dot-getseq_vectorized | Vectorized sequence extraction with getSeq |
| dot-load_genome_packages | Load installed BSgenome packages |
| dot-normalize_tm_gc_metadata | Normalize Tm/GC metadata column names on a GRanges object |
| dot-parse_coord_strings | Parse coordinate strings into a data frame |
| dot-salt_correct_vec | Vectorized salt correction over per-sequence GC percent and... |
| dot-spill_fasta | Stage sequences as a FASTA file so that workers read rather... |
| dot-tm_as_granges | Read 'regions' as an interval query against a GRanges source |
| dot-tm_complete_gr | Fill in a GRanges that carries sequences but not their... |
| dot-tm_finish | Compute Tm for one task's windows |
| dot-tm_match | Resolve one identifier against a source's own names |
| dot-tm_model | Apply the selected model to windows that already carry their... |
| dot-tm_offsets | Where a source's records sit in the coordinate system the... |
| dot-tm_regions | Resolve 'regions' against a source |
| dot-tm_run | Run the tasks and reassemble one profile |
| dot-tm_source | Classify the input and describe what it offers |
| dot-tm_task_bsgenome | One task against a BSgenome |
| dot-tm_task_fasta | One task against a FASTA file |
| dot-tm_tasks | Cut the requested regions into tasks |
| ecoli_rep_hotspots | E. coli K-12 MG1655 replication-associated hotspot... |
| fa_to_genomic_ranges | Convert FASTA file to GenomicRanges object |
| gc_content | Calculate G and C content of nucleotide sequences |
| generate_complement | Generate complementary sequence |
| integrate_granges | Integrate a Tm GRanges with multi-omic feature ranges |
| make_genomiccoord | Generate sliding-window genomic coordinate strings for Tm... |
| plot_genome_track | Plot genome tracks in linear or circular layout |
| plot_tm | Compare Tm distributions across groups |
| print.TmCalculator | Prints melting temperature from a 'TmCalculator' object |
| s2c | convert a string into a vector of characters |
| salt_correct | Corrections of melting temperature with salt concentration |
| thermodynamic_gc_params | Thermodynamic parameters for GC-based Tm calculation methods |
| thermodynamic_nn_params | Thermodynamic Tables for Nucleic Acid Hybridization |
| tm_calculate | Calculate melting temperature using multiple methods |
| TmCalculator-package | TmCalculator: Genome-Wide Nucleic Acid Melting Temperature... |
| tm_gc | Calculate the melting temperature using empirical formulas... |
| tm_nn | Calculate melting temperature using nearest neighbor... |
| tm_wallace | Calculate the melting temperature using the 'Wallace rule' |
| to_genomic_ranges | Convert input sequences to a GRanges object (fast backend) |
| vec_to_genomic_ranges | Convert sequence strings to GenomicRanges object |
