Man pages for vaulot/dvutils
A set of utilities
| blast_18S_reformat | Process a tabular output from blastn (BLAST+) |
| blast_summary | Write a summary for a tabular output from blastn (BLAST+) |
| colors_euk_class | Color for classes. |
| colors_euk_division | Color for divisions. |
| colors_euk_genus | Color for genera. |
| dada2_assign | Assign sequences using dada2 wang assigner |
| dada2_export | Export a data frame to dada2 AssignTaxonomy compatible format |
| db_append_records | Write new records to a table. |
| db_connect | Establish a connection database |
| db_connect_sqlite | Establish a connection to a SQLite database |
| db_disconnect | Disconnect an existing connection |
| db_execute_query_vector | Execute a vector of query. |
| db_get_query | Read a query into a dataframe. |
| db_info | Get the connection info for a specific database |
| db_sql_escape | Put a string between single quotes |
| db_update_field_string | Build a string to update a field in a database |
| fasta_filter | Filter a fasta file |
| fasta_read | Read a fasta file into a data frame |
| fasta_write | Write a fasta file with the taxonomy |
| fastq_subsample | Subsample fastq files |
| filename_append | Append a string at the end of a file name before the exension |
| filename_change_ext | Change the extension of the file name |
| file_unix2dos | Convert between Unix and Dos text format |
| genbank_download | Download sequences from GenBank |
| genbank_download_parse | Download and parse sequences from GenBank |
| genbank_download_parse_rentrez | Download and parse sequences from GenBank using rentrez only |
| genbank_features | Read features of sequences from GenBank |
| genbank_field | Read a single field from a set of existing GenBank files |
| genbank_locus | Read locus from a set of existing GenBank files |
| genbank_parse_rentrez_xml | Download and parse sequences from GenBank using rentrez and... |
| genbank_search | Search GenBank |
| genbank_taxonomy | Read NCBI taxo |
| get_primer_position | Get primer position on sequence set |
| gg_bar_discrete | Do a simple barplot |
| gg_boxplot | Plot a box plot |
| gg_density | Plot simple density plot to compare factors |
| gg_hist | Plot simple histogram |
| gg_violin | Plot a violin and a box plot |
| kmer | Get all kmers in a sequence |
| kmer_set | Get all kmers in a set of sequence |
| latex_fix_bibfile | Fix bib library file created by Mendeley |
| lat_long_dec | Convert lat and long to decimal |
| map_distribution | Draw distribution map from data frame |
| map_get_world | Get the world map for the rworldmap package |
| map_leaflet | Map with leaflet package (OpenStreetMap) |
| map_US | Background US map using the maps package to extract a... |
| map_world | Background map using the maps package |
| map_world_google | Background map using the ggmap package |
| map_zoom_europe | Zoom a map on Europe |
| metapr2_export_asv | Exports the metapr2 database |
| metapr2_export_datasets | Exports the metapr2_datasets table |
| metapr2_export_metadata | Exports the metapr2_metadata table |
| metapr2_export_qs | Exports the metapr2 database in qs file for shiny app |
| metapr2_export_reads_total | Exports the total number of reads in each dataset |
| pcr_sequences | In silico amplification |
| phyloseq_filter_abundant_taxa | Filter a phyloseq table keeping only abundant taxa |
| phyloseq_filter_autotrophic_taxa | Filter a phyloseq table keeping only autotrophic taxa |
| phyloseq_import_mothur | Create a phyloseq file from mothur database file |
| phyloseq_long_bargraph | Do a bar graph of top taxo_level or asvs based on the long... |
| phyloseq_long_treemap | Do a treemap based on the long version of a phyloseq file |
| phyloseq_nmds | Do a bar graph of top taxo_level or asvs based on the long... |
| phyloseq_normalize_median | Normalize to the median number of reads |
| phyloseq_normalize_percent | Normalize as percent of total reads |
| phyloseq_transform_to_long | Transform a phyloseq object into a long data frame |
| pr2_buid_taxons | Build taxon table (long format) |
| pr2_build_taxonomy | Buikd taxonomy table (wide format) from taxon table (long... |
| pr2_colors_read | Reads the PR2 color into a data frame |
| pr2_export | Export the PR2 database (one file) |
| pr2_export_all | Export the PR2 database (all files) |
| pr2_export_sqlite | Export the PR2 database to a SQLite file |
| pr2_extract_one_taxo_level | Extract one level of taxonomy |
| pr2_read | Reads the whole PR2 database into a data frame |
| pr2_sequence_label | Create a simple label for a sequence |
| pr2_taxo_check | Check taxonomy |
| pr2_taxo_list | Build a list of taxa |
| pr2_taxo_read | Reads the PR2 taxonomic database into a data frame |
| pr2_taxo_X | Add _X for taxon that are repeated on same line |
| pr2_traits_read | Reads the PR2 traits database into a data frame |
| pr2_treemap | Draw a simple treemap from pr2. |
| rcc_customers | Format "customers.csv" for import into rcc database |
| rcc_export | Export tables from MySQL database |
| rcc_genbank | Prepare list of GenBank entries to include in rcc database |
| rcc_order_details | Format "order_details.csv" for import into rcc database |
| rcc_orders | Format "orders.csv" for import into rcc database |
| seq_reverse_complement | Reverse complement string |
| theme_dviz_grid | Theme - grid lines along major axis ticks, no axes |
| theme_dviz_hgrid | Theme - horizontal grid lines only |
| theme_dviz_vgrid | Theme - vertical grid lines only |
| treemap_dv | Do a simple treemap |
| unfill | Remove repeated values in vector |
| XStringSet_to_df | Transforms a DNA or AA String set into a data frame |
