Man pages for kkrismer/transite
RNA-binding protein motif analysis

calculate_kmer_enrichment_k_-mer Enrichment between Foreground and Background Sets
calculate_local_consistencyLocal Consistency Score
calculate_motif_enrichmentBinding Site Enrichment Value Calculation
calculate_transcript_mcMotif Enrichment calculation
check_kmersCheck Validity of Set of _k_-mers
classify_spectrumSimple spectrum classifier based on empirical thresholds
compute_kmer_enrichment_k_-mer Enrichment between Foreground and Background Sets
count_homopolymer_corrected_kmersCorrection for Homopolymeric Stretches
create_kmer_motifCreates Transite motif object from character vector of...
create_kmer_origin_listCreate _k_-mer lists with their original sequences
create_matrix_motifCreates Transite motif object from position weight matrix
draw_volcano_plot_k_-mer Enrichment Volcano Plot
estimate_significancePermutation Test Based Significance of Observed Mean
estimate_significance_coreSignificance of Observed Mean
geToy Gene Expression Data Set
generate_iupac_by_kmersGenerates IUPAC code for a character vector of _k_-mers
generate_iupac_by_matrixGenerates IUPAC code for motif matrix
generate_kmers_k_-mer Counts for Sequence Set
generate_kmers_from_iupacGenerates all _k_-mers for IUPAC string
generate_permuted_enrichmentsGenerate Random Permutations of the Enrichment Data
geometric_meanGeometric Mean
get_motif_by_idRetrieve motif objects by id
get_motif_by_rbpRetrieve motif objects by gene symbol
get_motifsRetrieve list of all motifs
get_motifs_meta_infoDisplays motif meta information.
get_ppmGet Position Probability Matrix (PPM) from motif object
init_iupac_lookup_tableInitializes the IUPAC lookup table
kmers_enrichmentExample _k_-mer Enrichment Data
motifsTransite Motif Database
p_combineP-value aggregation
RBPMotif-classAn S4 class to represent a RBPMotif
run_kmer_spma_k_-mer-based Spectrum Motif Analysis
run_kmer_tsma_k_-mer-based Transcript Set Motif Analysis
run_matrix_spmaMatrix-based Spectrum Motif Analysis
run_matrix_tsmaMatrix-based Transcript Set Motif Analysis
score_sequencesScore Sequences with PWM
score_spectrumCalculates spectrum scores and creates spectrum plots
score_transcriptsScores transcripts with position weight matrices
score_transcripts_single_motifScores transadsadscripts with position weight matrices
set_motifsSet Transite motif database
SpectrumScore-classAn S4 class to represent a scored spectrum
subdivide_dataSubdivides Sequences into _n_ Bins
toy_motif_matrixToy Motif Matrix
transitetransite
kkrismer/transite documentation built on July 13, 2024, 8:01 a.m.