Files in HajkD/metablastr

Perform Massive Local BLAST Searches

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.gitignore

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/blast2bed.R R/blast_best_hit.R R/blast_best_reciprocal_hit.R R/blast_genomes.R R/blast_nucleotide_to_genomes.R R/blast_nucleotide_to_nucleotide.R R/blast_nucleotide_to_protein.R R/blast_outfmt_colnames.R R/blast_outfmt_colnames_databases.R R/blast_protein_to_nr_database.R R/blast_protein_to_nucleotide.R R/blast_protein_to_protein.R R/blast_protein_to_proteomes.R R/blast_repbase.R R/blast_rpsblast.R R/detect_homologs_cds_to_cds.R R/detect_homologs_proteome_to_proteome.R R/extract_hit_seqs_from_genomes.R R/extract_promotor_seqs_from_genome.R R/extract_random_seqs_from_genome.R R/extract_random_seqs_from_multiple_genomes.R R/extract_upstream_promotor_seqs.R R/file_contains_aa.R R/file_contains_dna.R R/filter_best_hits.R R/filter_homologs_core_set.R R/filter_homologs_core_set_n_species.R R/gg_blast_hits.R R/gg_blast_hits_summary.R R/gg_hits_boxplot.R R/gg_homologs_one_to_one.R R/gg_pairwise_orthologs_line.R R/gg_shared_genes.R R/gg_shared_splice_variants.R R/gg_species_dnds_blast_tbl.R R/gg_species_feature_blast_tbl.R R/gg_species_promotor_dist_blast_tbl.R R/is_blast_installed.R R/is_outformat.R R/is_samtools_installed.R R/list_outformats.R R/motif_compare.R

R/motif_compare_multi.R

R/motif_compare_multi_promotor_seqs.R R/motif_count.R R/motif_count_matrix.R R/motif_enrichment.R R/motif_enrichment_multi.R R/motif_enrichment_multi_promotor_seqs.R R/outformat2num.R R/read_blast.R R/read_blast_databases.R R/remove_multipart_transcripts.R R/sample_chromosome_intervals.R R/ws_wrap.R README.md

docs/404.html

docs/LICENSE-text.html

docs/articles/index.html

docs/articles/installation.html

docs/articles/installation_files/accessible-code-block-0.0.1/empty-anchor.js

docs/articles/installation_files/anchor-sections-1.0/anchor-sections.css

docs/articles/installation_files/anchor-sections-1.0/anchor-sections.js

docs/authors.html

docs/bootstrap-toc.css

docs/bootstrap-toc.js

docs/docsearch.css

docs/docsearch.js

docs/index.html

docs/jquery.sticky-kit.min.js

docs/link.svg

docs/news/index.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/Rplot001.png

docs/reference/blast2bed.html

docs/reference/blast_best_hit.html

docs/reference/blast_best_reciprocal_hit.html

docs/reference/blast_genomes.html

docs/reference/blast_nucleotide_to_genomes.html

docs/reference/blast_nucleotide_to_nucleotide.html

docs/reference/blast_nucleotide_to_protein.html

docs/reference/blast_protein_to_nr_database.html

docs/reference/blast_protein_to_nucleotide.html

docs/reference/blast_protein_to_protein.html

docs/reference/blast_protein_to_proteomes.html

docs/reference/blast_repbase.html

docs/reference/blast_rpsblast.html

docs/reference/detect_homologs_cds_to_cds.html

docs/reference/detect_homologs_proteome_to_proteome.html

docs/reference/extract_hit_seqs_from_genomes.html

docs/reference/extract_promotor_seqs_from_genome.html

docs/reference/extract_random_seqs_from_genome.html

docs/reference/extract_random_seqs_from_multiple_genomes.html

docs/reference/extract_upstream_promotor_seqs.html

docs/reference/file_contains_aa.html

docs/reference/file_contains_dna.html

docs/reference/filter_best_hits.html

docs/reference/filter_homologs_core_set.html

docs/reference/filter_homologs_core_set_n_species.html

docs/reference/gg_blast_hits.html

docs/reference/gg_blast_hits_summary.html

docs/reference/gg_hits_boxplot.html

docs/reference/gg_homologs_one_to_one.html

docs/reference/gg_pairwise_orthologs_line.html

docs/reference/gg_species_dnds_blast_tbl.html

docs/reference/gg_species_feature_blast_tbl.html

docs/reference/gg_species_promotor_dist_blast_tbl.html

docs/reference/index.html

docs/reference/list_outformats.html

docs/reference/motif_compare.html

docs/reference/motif_compare_multi.html

docs/reference/motif_compare_multi_promotor_seqs.html

docs/reference/motif_count.html

docs/reference/motif_count_matrix.html

docs/reference/motif_enrichment.html

docs/reference/motif_enrichment_multi.html

docs/reference/motif_enrichment_multi_promotor_seqs.html

docs/reference/read_blast.html

docs/reference/read_blast_databases.html

docs/reference/sample_chromosome_intervals.html

docs/sitemap.xml

inst/seqs/qry_aa.fa

inst/seqs/qry_nn.fa

inst/seqs/sbj_aa.fa

inst/seqs/sbj_nn.fa

inst/seqs/sbj_nn_best_hit.fa

man/blast2bed.Rd man/blast_best_hit.Rd man/blast_best_reciprocal_hit.Rd man/blast_genomes.Rd man/blast_nucleotide_to_genomes.Rd man/blast_nucleotide_to_nucleotide.Rd man/blast_nucleotide_to_protein.Rd man/blast_protein_to_nr_database.Rd man/blast_protein_to_nucleotide.Rd man/blast_protein_to_protein.Rd man/blast_protein_to_proteomes.Rd man/blast_repbase.Rd man/blast_rpsblast.Rd man/detect_homologs_cds_to_cds.Rd man/detect_homologs_proteome_to_proteome.Rd man/extract_hit_seqs_from_genomes.Rd man/extract_promotor_seqs_from_genome.Rd man/extract_random_seqs_from_genome.Rd man/extract_random_seqs_from_multiple_genomes.Rd man/extract_upstream_promotor_seqs.Rd man/file_contains_aa.Rd man/file_contains_dna.Rd man/filter_best_hits.Rd man/filter_homologs_core_set.Rd man/filter_homologs_core_set_n_species.Rd man/gg_blast_hits.Rd man/gg_blast_hits_summary.Rd man/gg_hits_boxplot.Rd man/gg_homologs_one_to_one.Rd man/gg_pairwise_orthologs_line.Rd man/gg_species_dnds_blast_tbl.Rd man/gg_species_feature_blast_tbl.Rd man/gg_species_promotor_dist_blast_tbl.Rd man/list_outformats.Rd man/motif_compare.Rd man/motif_compare_multi.Rd man/motif_compare_multi_promotor_seqs.Rd man/motif_count.Rd man/motif_count_matrix.Rd man/motif_enrichment.Rd man/motif_enrichment_multi.Rd man/motif_enrichment_multi_promotor_seqs.Rd man/read_blast.Rd man/read_blast_databases.Rd man/sample_chromosome_intervals.Rd tests/testthat.R tests/testthat/test-file_contains.R tests/testthat/test-list_outformats.R tests/testthat/test-outformat2num.R

HajkD/metablastr documentation built on Sept. 14, 2023, 5:26 p.m.