align_alleles | Align allele sequences across loci |
allele_match | Check Sample Data for Potential Allele Matches |
analyze_dataset | Analyze all samples in a dataset |
analyze_sample | Analyze sequence table and categorize sequences |
analyze_seqs | Analyze a set of STR sequences |
apply_config | Apply CHIIMP options globally |
calc_genotype_distance | Calculate distance between two genotypes |
categorize_genotype_results | Categorize genotyping results |
cfg | Get/set CHIIMP global configuration options |
CFG_DEFAULTS | Default Configuration |
check_length | Check sequences for expected length |
check_motif | Check sequences for STR repeats |
chiimp-package | CHIIMP |
CMP | Complements of IUPAC nucleotide codes |
find_artifact | Check for non-stutter PCR artifacts between sequences |
find_closest_matches | Find closest matches in distance matrix |
find_primer_matches | Find primer matches for reads |
find_stutter | Check for PCR stutter between sequences |
format_pandoc_args | Create Pandoc Metadata Argument Strings |
full_analysis | Perform a full microsatellite analysis |
get_px_width | Get plot unit width |
handle_primers | Modify reads based on matched primers |
histogram | Plot histogram of STR sequences |
load_allele_names | Load table of known allele names |
load_config | Load configuration file |
load_config_csv | Load configuration file from CSV |
load_config_yaml | Load configuration file from YAML |
load_csv | Load and save tables from CSV |
load_dataset | Load table of sample attributes |
load_genotypes | Load table of genotypes |
load_locus_attrs | Load table of locus attributes |
load_seqs | Load vector of sequences from FASTA/FASTQ file |
logmsg | Write Log Message |
main | Handle full microsatellite analysis from command-line |
make_allele_names | Create Short Allele Names |
make_dist_mat | Make distance matrix for set of samples |
make_dist_mat_known | Make distance matrix for samples to known genotypes |
make_entry_id | Create identifiers for STR Data |
make_raw_nt | Make matrix of raw bytes from nucleotide sequences |
make_read_primer_table | Make data frame of primer info for reads |
make_rownames | Create Row Names for STR Data |
match_known_genotypes | Associate known genotypes with samples |
name_alleles_in_table | Name allele sequences in genotype data frame |
name_known_sequences | Name known allele sequences |
order_entries | Define Ordering for STR Data |
parse_config | Parse a configuration data frame into list |
plot_alignment | Plot Sequence Alignments |
plot_cts_per_locus | Plot heatmap of read counts matching each locus primer |
plot_dist_mat | Plot Distance Matrix |
plot_heatmap | Render heatmap of STR attribute across samples and loci |
plot_heatmap_artifacts | Plot heatmap of suspected PCR artifacts |
plot_heatmap_homozygous | Plot heatmap of homozygous samples |
plot_heatmap_prominent_seqs | Plot heatmap of samples with multiple prominent sequences |
plot_heatmap_proportions | Plot heatmap of proportion of allele sequence counts |
plot_heatmap_stutter | Plot heatmap of suspected PCR stutter |
prepare_dataset | Extract Sample Attributes from Filenames |
RAW_NT | IUPAC DNA nucleotides as raw bytes |
remove_shared_root_dir | Remove shared path from file paths |
render_report | Render Microsatellite Report Document |
report_genotypes | Create genotype summary table |
report_idents | Create identification summary table |
revcmp | Reverse complement sequences |
sample_analysis_funcs | Versions of analyze_sample |
sample_summary_funcs | Versions of summarize_sample |
save_alignment_images | Save alignment visualizations to image files |
save_alignments | Save alignments to FASTA files |
save_allele_seqs | Save identified alleles to FASTA files |
save_data | Save Microsatellite Analysis to Disk |
save_dataset | Save table of sample attributes |
save_dist_mat | Save sample distance matrix to text file |
save_histograms | Save sequence histogram visualizations to image files |
save_results_summary | Save dataset summary to text file |
save_sample_data | Save per-sample processed data to text files |
save_seqfile_data | Save per-file processed data to text files |
setup_package | Set up CHIIMP package environment |
sort_results | Sort entries in results data frames |
str_hist_render | Draw prepared histogram data |
str_hist_setup | Prepare histogram data |
str_hist_setup_legend | Setup display attributes for STR histogram |
summarize_attribute | Create Summary Attribute Table |
summarize_dataset | Add further summaries to analyzed dataset |
summarize_genotypes | Create Summary Genotype Table |
summarize_genotypes_known | Create Summary Genotype Table for Known Genotypes |
summarize_sample | Summarize a processed STR sample |
tabulate_allele_names | Wide table of allele names vs loci |
tally_cts_per_locus | Create Counts-per-Locus Table |
test_data | Helper Data for Examples |
tidy_analyzed_dataset | Tidy raw analyzed dataset results |
version_compare | Compare two version strings |
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.