Man pages for ShawHahnLab/chiimp
Computational, High-throughput Individual Identification through Microsatellite Profiling

align_allelesAlign allele sequences across loci
allele_matchCheck Sample Data for Potential Allele Matches
analyze_datasetAnalyze all samples in a dataset
analyze_sampleAnalyze a set of STR sequences
calc_genotype_distanceCalculate distance between two genotypes
check_lengthCheck sequences for expected length
check_motifCheck sequences for STR repeats
chiimp-packageAnalyze Microsatellites
config.defaultsDefault microsatellite configuration
find_artifactCheck for non-stutter PCR artifacts between sample entries
find_closest_matchesFind closest matches in distance matrix
find_matching_primerLabel STR sample rows by locus
find_stutterCheck for PCR stutter between sample entries
format_pandoc_argsCreate Pandoc Metadata Argument Strings
full_analysisPerform a full microsatellite analysis
histogramPlot basic histogram of STR sample
histogram2Plot advanced histogram of STR sample
load_allele_namesLoad table of known allele names
load_configLoad configuration file
load_datasetLoad table of sample attributes
load_genotypesLoad table of genotypes
load_locus_attrsLoad table of locus attributes
load_seqsLoad vector of sequences from FASTA/FASTQ file
logmsgWrite Log Message
mainHandle full microsatellite analysis from command-line
make_allele_nameCreate Short Allele Names
make_dist_matMake distance matrix for set of samples
make_dist_mat_knownMake distance matrix for samples to known genotypes
make_entry_idCreate identifiers for STR Data
make_rownamesCreate Row Names for STR Data
order_entriesDefine Ordering for STR Data
plot_alignmentPlot Sequence Alignments
plot_cts_per_locusPlot heatmap of read counts matching each locus primer
plot_dist_matPlot Distance Matrix
plot_heatmapRender heatmap of STR attribute across samples and loci
plot_heatmap_artifactsPlot heatmap of suspected PCR artifacts
plot_heatmap_homozygousPlot heatmap of homozygous samples
plot_heatmap_prominent_seqsPlot heatmap of samples with multiple prominent sequences
plot_heatmap_proportionsPlot heatmap of proportion of allele sequence counts
plot_heatmap_stutterPlot heatmap of suspected PCR stutter
prepare_datasetExtract Sample Attributes from Filenames
render_reportRender Microsatellite Report Document
report_genotypesCreate genotype summary table
report_identsCreate identification summary table
save_alignment_imagesSave alignment visualizations to image files
save_alignmentsSave alignments to FASTA files
save_allele_seqsSave identified alleles to FASTA files
save_dataSave Microsatellite Analysis to Disk
save_dist_matSave sample distance matrix to text file
save_histogramsSave sequence histogram visualizations to image files
save_results_summarySave dataset summary to text file
save_sample_dataSave per-sample processed data to text files
summarize_attributeCreate Summary Attribute Table
summarize_datasetAdd further summaries to analyzed dataset
summarize_genotypesCreate Summary Genotype Table
summarize_genotypes_knownCreate Summary Genotype Table for Known Genotypes
summarize_sampleSummarize a processed STR sample
summarize_sample_by_lengthSummarize a processed STR sample, Length Version
summarize_sample_guidedSummarize a processed STR sample Using Known Lengths
summarize_sample_naiveSummarize a processed STR sample, Simple Version
tally_cts_per_locusCreate Counts-per-Locus Table
tidy_analyzed_datasetTidy raw analyzed dataset results
ShawHahnLab/chiimp documentation built on April 8, 2018, 3:36 p.m.