Man pages for brouwern/compbio4all
Datasets and helpful functions for learning bioinformatics and computational biology
| aa_chars | Characteristics of amino acids |
| aa_chars_subset | Characteristics of amino acids (subset) |
| aa_dat | Dataset helpfile header . . . |
| antlers | Simulated data on the effects of diet on deer antlers |
| AOU_species_codes | American Ornithological Union (AOU) species codes for... |
| BBS_PA | Pennsylvania Breeding Survey Data (BBS) from the USGS. |
| BBS_PA_combo_cover_1km | Combinations of NLCD land cover classes into more general... |
| BBS_PA_landcover_1km | Land cover buffers from the 1 km surrounding Breeding Bird... |
| BBS_PA_SCTA | Number of Scarlet tanagers (SCTA) observed on Pennsylvania... |
| blastr | Execute BLAST from R. |
| brook_trout | Brook trout impacts on Chinook salmon survival - original... |
| brook_trout_ABD | Impact of brook trout on survival of Chinook salmon in Idaho. |
| chargaff1951 | Data from publications by Chargaff 1951 |
| clean_alignment | Print multiple sequence alignment (MSA) to R console |
| combine_NLCD_classes | Combine multiple landcover classes into a single combined... |
| compbio4all-package | compbio4all: Datasets and helpful functions for learning... |
| dengueseq_fasta | dengueseq_fasta |
| dengueseqstartstring | Data for computational gene finding exercise |
| diag_show | Print the diagonal of a matrix |
| dmshrm_blast_1 | BLAST results obtained from bio3d::blast.pdb(). blast.pdb()... |
| dmshrm_blast_2 | BLAST results obtained with the blastr() function |
| dna_seq_stringset | Stringset of four mRNA sequences from dengue fever-related... |
| doves_PA | PA Mourning doves |
| doves_PA_3_years | PA Mourning doves from 3 years, 2005, 2007 and 2010 |
| eaglesOH | Eagles in Ohio dataset |
| eaglesPA | Eagles in Pennsylvania dataset |
| eaglesWV | Eagles in West Virginia (WV) dataset#' A dataset containing... |
| eggs | Bird eggs datatset. |
| eggs_and_nests | Egg data combined with data on nests |
| eggs_and_nests2 | Subset of eggs_and_nests data the contains only Dome, Cup,... |
| ensemblleishmania | Leishmania output from ENSEMBL |
| ensemblpfalciparum | Plasmodium falciparum-related datasets |
| entrez_fetch_list | Process multiple NCBI accessions and output as list |
| expand_BBS_routes | Expand BBS data to include zeros when a species was not seen. |
| fasta_cleaner | Function to convert a FASTA file stored as an object into a... |
| find_ORFs_in_seq | Find potential open reading frames (ORFs) in a DNA sequence. |
| find_start_stop_codons | Function to identify potential start and stop codons |
| frogarms | Data on the body size and arm girth of male and female... |
| generate_hmm_seq | Function to generate a DNA sequence, given a HMM and the... |
| generate_markov_seq | Generate a DNA sequence using a Markov Chain. |
| genes_dpc | Dataset helpfile header . . . |
| genes_hpc | Dataset helpfile header . . . |
| genes_mpc | Dataset helpfile header . . . |
| hShroom2 | hShroom2 |
| hShroom3 | hShroom3 |
| human_bodytemp | Human body temperature data and heartrate |
| human_gene_lengths | Lengths of human genes |
| leishmaniagenes | Leishmaniabgenes output from ENSEMBL |
| leishmaniagenes2 | Subset of Leishmania genes output from ENSEMBL |
| make_dateset_helpfile | Create template for dataset documentation |
| make_my_data2L | Extract random subset of a dataframe |
| make_seqs_multinom_mod | make_seqs_multinom_mod |
| make_viterbi_mat | Function to generate a DNA sequence, given a HMM and the... |
| martin1995 | Dataset helpfile header . . . |
| milk | Mammal milk dataset |
| mShroom3a | mShroom3a |
| NA_to_zero | Change all NA values (missing vlaues) in a column to zero |
| pams | Point-accepted mutation (PAM) data matrix from Dayoff et al.... |
| pfalciparumgenes | Plasmodium falciparum-related datasets |
| pikas | Data on presence of pikas and marmots from Front Range Pika... |
| plot_ORFs_in_seq | Find and plot potential ORFs |
| plot_sliding_window | plot_sliding_window |
| plot_start_stop_codons | plot_potential_starts_and_stops |
| print_msa | Print multiple sequence alignment (MSA) to R console |
| print_pairwise_alignment | printPairwiseAlignment |
| robinson_aafreq | Dataset helpfile header . . . |
| rooted_NJ_tree | Wrapper function for creating rooted neighbor-joining trees |
| sample_BBS_routes | Select random subset of Breeding Bird Survey (BBS) routes |
| sample_dove_routes | Select random subset of Breeding Bird Survey (BBS) routes |
| score_alignment | Score a simple alignment |
| seq_1_2_3_4 | seq_1_2_3_4 |
| seq_1_2_3_4_stringset | seq_1_2_3_4_stringset |
| shroom_table | shroom_table |
| sShroom | sShroom |
| trillium | Data on the size of Trillium from several sites in Crawford... |
| tri_print | Print the lower or upper triangular part of a matrix... |
| virusaln | Alignment of four proteins from dengue fever-related viruses |
| virusaln_seqinr | Alignment of four proteins from dengue fever-related viruses... |
| virusaln_seqinr_clean | Alignment of four proteins from dengue fever-related viruses... |
| virus_mrna_aln | Alignment of four mRNA sequences from dengue fever-related... |
| virus_mrna_aln_bin | Alignment of four proteins from dengue fever-related viruses... |
| virus_mrna_dist | Distance matrix of Dengue virus mRNA sequences |
| virus_snc | Dataset helpfile header . . . |
| virus_snr | Dataset helpfile header . . . |
| viterbi | By Coghlan (2011), adapted from "Applied Statistics for... |
| wetlands | Data on species richness in constructed wetlands at... |
| wine | Wine recognition data |
| woodcock_MI_3_years | Subset of Woodcock call survey data from Michigan, USA |
