Files in lijing28101/fagin2

Annotate Orphan Genes

R/class.R R/class_summarize.R R/comparison.R R/fagin.R R/fagin_new_gene.R R/fagin_parallel.R R/feature_table.R R/functions_alignments.R R/functions_derive.R R/functions_indels.R R/functions_overlaps.R R/gff_handle.R R/hits_info.R R/load_species.R R/util.R R/z_nucleotide.R R/z_protein.R R/z_tree.R README.md man/AA_aln.Rd man/MakeGI.Rd man/add_gene.Rd man/alignToGenome.Rd man/align_by_map.Rd man/aln_xy.Rd man/buildFeatureTable.Rd man/buildLabelsTree.Rd man/calculate_match_significance.Rd man/check_for_incomplete_models.Rd man/check_for_internal_stops.Rd man/check_protein_transcript_match.Rd man/compare_target_to_focal.Rd man/config.Rd man/config_alignment-class.Rd man/config_alignment_alnrate-class.Rd man/config_alignment_pvalue-class.Rd man/config_alignment_simulation-class.Rd man/config_input-class.Rd man/config_orf-class.Rd man/config_synder-class.Rd man/convert_FaFile_to_XStringSet.Rd man/convert_GRanges_to_SynderGFF.Rd man/derive_genomic_ORFs.Rd man/derive_nstring.Rd man/derive_transcript_ORFs.Rd man/derived_input-class.Rd man/dgumbel.Rd man/dna_summary-class.Rd man/dnaregex.Rd man/dot-dnaregex_unstranded.Rd man/dot-label.Rd man/extract_phase_from_GRangesList.Rd man/extract_range.Rd man/extract_with_complements.Rd man/faa_summary-class.Rd man/fagin_config-class.Rd man/fagin_io.Rd man/fagin_summary.Rd man/filter_with_warning__unnamed_entries.Rd man/filter_with_warnings__zero_length_proteins.Rd man/find_indels.Rd man/fit.gumbel.Rd man/fix_names.Rd man/fuzzy_translate.Rd man/gene_check.Rd man/getORFs.Rd man/get_alignment_table.Rd man/get_dna2dna.Rd man/get_gff_from_txdb.Rd man/get_hits_info.Rd man/get_logmn.Rd man/get_query_position.Rd man/get_species.Rd man/get_target_mRNA_position.Rd man/get_target_position.Rd man/get_trans_dna.Rd man/gff_summary-class.Rd man/granges_summary-class.Rd man/labelTreeToTable.Rd man/load_gene_models.Rd man/load_species.Rd man/make_seqinfo.Rd man/merge_feature_table.Rd man/numeric_summary-class.Rd man/overlapMap.Rd man/pgumbel.Rd man/phase_summary-class.Rd man/qgumbel.Rd man/run_fagin.Rd man/run_fagin_add.Rd man/run_fagin_parallel.Rd man/secondary_data.Rd man/secondary_data_add.Rd man/seq_summary-class.Rd man/species_data_files-class.Rd man/species_meta-class.Rd man/species_summaries-class.Rd man/synmap_summary-class.Rd man/synteny_meta-class.Rd man/trim_CDS_with_non_zero_phase.Rd man/validate_config.Rd