Man pages for HajkD/orthologr
Comparative Genomics with R

blastPerform a BLAST+ search
blast_bestPerform a BLAST+ best hit search
blast_recPerform a BLAST+ reciprocal best hit (RBH) search
cds2aaTranslate CDS file to Amino Acids file
clean_all_foldersDelete the internal folder hierarchy
codon_alnCompute a Codon Alignment
compute_dndsCompute dNdS Values For A Given Pairwise Alignment
divergence_mapSort dNdS Values Into Divergence Strata
divergence_stratigraphyPerform Divergence Stratigraphy
dNdSCompute dNdS values for two organisms
extract_featuresHelper function to extract gene loci and splice variant IDs...
filter_best_hitsHelper function to select best BLAST hit based on minimum...
filter_core_setHelper function to extract a core set of orthologous gene...
filter_core_set_lncHelper function to extract a core set of orthologous lncRNAs
filter_dNdSFilter dNdS values
generate_ortholog_tablesGenerate ortholog tables by gene locus and splice varaint
generate_ortholog_tables_allGenerate ortholog tables by gene locus and splice varaint for...
import_ortholog_tables_allImporting output pairwise orthologs tables generated with...
lnc_map_core_orthologsRetrieve a core set of orthologous lncRNAs from the pairwise...
lnc_map_countsCount number of orthologous lncRNAs per pairwise species...
map_generator_dndsGenerate dNdS Maps Between a Query Organism and Multiple...
map_generator_lncInfer orthologous lncRNAs between multiple species
multi_alnCompute Multiple Sequence Alignments
orthofinder2Interface function to Orthofinder2
orthofinder2_retrieve_core_orthologsRetrieve core orthologs across multiple species from...
orthologsMain Orthology Inference Function
orthologs_lncOrthology Inference of lncRNAs
pairwise_alnCompute Pairwise Alignments
plot_diverse_homology_thresholdsDiverse line plots visualizing the number of pairwise...
plot_diverse_homology_thresholds_core_orthologsDiverse line plots visualizing the number of core orthologs...
plot_pairwise_orthologsA line plot visualizing the number of pairwise orthologs...
read.cdsRead the CDS of a given organism
read.dnds.tblImport a dNdS table generated with 'dNdS'
read.genomeRead the genome of a given organism
read.proteomeRead the proteome of a given organism
retrieve_core_orthologsRetrieve a core set of orthologous gene loci from several...
retrieve_longest_isoformsRetrieve the longest isoforms from a proteome file and save...
retrieve_longest_isoforms_allRetrieve the longest isoforms of several proteome files...
select_orthologsSelect orthologs based on either gene locus or splice variant
set_blastCreate a BLASTable database with makeblastdb
substitutionrateInternal function for dNdS computations
testCoreOrthoParamsGeneLocusHelper function for...
testCoreOrthoParamsSpliceVariantHelper function for...
translTranslate DNA to Amino Acids
translate_cds_to_proteinTranslate coding sequences into amino acid sequences
translate_cds_to_protein_allTranslate coding sequences into amino acid sequences for...
write.proteomeSave a proteome in fasta format
HajkD/orthologr documentation built on Nov. 6, 2019, 10:55 a.m.