Package: transite 1.25.0
Konstantin Krismer
transite: RNA-binding protein motif analysis
transite is a computational method that allows comprehensive analysis of the regulatory role of RNA-binding proteins in various cellular processes by leveraging preexisting gene expression data and current knowledge of binding preferences of RNA-binding proteins.
Authors:
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transite.pdf |transite.html✨
transite/json (API)
NEWS
| # Install 'transite' in R: |
| install.packages('transite', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
- ge - Toy Gene Expression Data Set
- kmers_enrichment - Example _k_-mer Enrichment Data
- motifs - Transite Motif Database
- toy_motif_matrix - Toy Motif Matrix
On BioConductor:transite-1.25.0(bioc 3.21)transite-1.24.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
geneexpressiontranscriptiondifferentialexpressionmicroarraymrnamicroarraygeneticsgenesetenrichment
Last updated 25 days agofrom:9b520b8ea4. Checks:OK: 1 NOTE: 3 WARNING: 5. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Oct 31 2024 |
| R-4.5-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.5-linux-x86_64 | NOTE | Oct 31 2024 |
| R-4.4-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.4-mac-x86_64 | WARNING | Oct 31 2024 |
| R-4.4-mac-aarch64 | NOTE | Oct 31 2024 |
| R-4.3-win-x86_64 | WARNING | Oct 31 2024 |
| R-4.3-mac-x86_64 | WARNING | Oct 31 2024 |
| R-4.3-mac-aarch64 | NOTE | Oct 31 2024 |
Exports:calculate_kmer_enrichmentcalculate_local_consistencycalculate_motif_enrichmentcalculate_transcript_mccheck_kmersclassify_spectrumcompute_kmer_enrichmentcreate_kmer_motifcreate_matrix_motifdraw_volcano_plotestimate_significanceestimate_significance_coregenerate_iupac_by_kmersgenerate_iupac_by_matrixgenerate_kmersgenerate_kmers_from_iupacgenerate_permuted_enrichmentsgeometric_meanget_adj_r_squaredget_consistency_scoreget_consistency_score_nget_consistency_score_p_valueget_heptamersget_hexamersget_idget_iupacget_model_degreeget_model_f_statisticget_model_f_statistic_p_valueget_model_residualsget_model_slopeget_motif_by_idget_motif_by_rbpget_motif_matrixget_motifsget_motifs_meta_infoget_ppmget_rbpsget_sourceget_speciesget_typeget_widthinit_iupac_lookup_tablep_combineplotrun_kmer_spmarun_kmer_tsmarun_matrix_spmarun_matrix_tsmascore_sequencesscore_spectrumscore_transcriptsset_motifssubdivide_data
Dependencies:askpassBiocGenericsBiostringsclicolorspacecrayoncurldplyrfansifarvergenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesggplot2gluegridExtragtablehttrIRangesisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmeopensslpillarpkgconfigR6RColorBrewerRcpprlangS4VectorsscalessysTFMPvaluetibbletidyselectUCSC.utilsutf8vctrsviridisLitewithrXVectorzlibbioc
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| _k_-mer Enrichment between Foreground and Background Sets | calculate_kmer_enrichment |
| Local Consistency Score | calculate_local_consistency |
| Binding Site Enrichment Value Calculation | calculate_motif_enrichment |
| Motif Enrichment calculation | calculate_transcript_mc |
| Check Validity of Set of _k_-mers | check_kmers |
| Simple spectrum classifier based on empirical thresholds | classify_spectrum |
| _k_-mer Enrichment between Foreground and Background Sets | compute_kmer_enrichment |
| Correction for Homopolymeric Stretches | count_homopolymer_corrected_kmers |
| Creates Transite motif object from character vector of _k_-mers | create_kmer_motif |
| Creates Transite motif object from position weight matrix | create_matrix_motif |
| _k_-mer Enrichment Volcano Plot | draw_volcano_plot |
| Permutation Test Based Significance of Observed Mean | estimate_significance |
| Significance of Observed Mean | estimate_significance_core |
| Toy Gene Expression Data Set | ge |
| Generates IUPAC code for a character vector of _k_-mers | generate_iupac_by_kmers |
| Generates IUPAC code for motif matrix | generate_iupac_by_matrix |
| _k_-mer Counts for Sequence Set | generate_kmers |
| Generates all _k_-mers for IUPAC string | generate_kmers_from_iupac |
| Generate Random Permutations of the Enrichment Data | generate_permuted_enrichments |
| Geometric Mean | geometric_mean |
| Retrieve motif objects by id | get_motif_by_id |
| Retrieve motif objects by gene symbol | get_motif_by_rbp |
| Retrieve list of all motifs | get_motifs |
| Displays motif meta information. | get_motifs_meta_info |
| Get Position Probability Matrix (PPM) from motif object | get_ppm |
| Initializes the IUPAC lookup table | init_iupac_lookup_table |
| Example _k_-mer Enrichment Data | kmers_enrichment |
| Transite Motif Database | motifs |
| P-value aggregation | p_combine |
| An S4 class to represent a RBPMotif | .RBPMotif get_heptamers get_heptamers,RBPMotif-method get_hexamers get_hexamers,RBPMotif-method get_id get_id,RBPMotif-method get_iupac get_iupac,RBPMotif-method get_motif_matrix get_motif_matrix,RBPMotif-method get_rbps get_rbps,RBPMotif-method get_source get_source,RBPMotif-method get_species get_species,RBPMotif-method get_type get_type,RBPMotif-method get_width get_width,RBPMotif-method RBPMotif-class show,RBPMotif-method |
| _k_-mer-based Spectrum Motif Analysis | run_kmer_spma |
| _k_-mer-based Transcript Set Motif Analysis | run_kmer_tsma |
| Matrix-based Spectrum Motif Analysis | run_matrix_spma |
| Matrix-based Transcript Set Motif Analysis | run_matrix_tsma |
| Score Sequences with PWM | score_sequences |
| Calculates spectrum scores and creates spectrum plots | score_spectrum |
| Scores transcripts with position weight matrices | score_transcripts |
| Scores transadsadscripts with position weight matrices | score_transcripts_single_motif |
| Set Transite motif database | set_motifs |
| An S4 class to represent a scored spectrum | .SpectrumScore get_adj_r_squared get_adj_r_squared,SpectrumScore-method get_consistency_score get_consistency_score,SpectrumScore-method get_consistency_score_n get_consistency_score_n,SpectrumScore-method get_consistency_score_p_value get_consistency_score_p_value,SpectrumScore-method get_model_degree get_model_degree,SpectrumScore-method get_model_f_statistic get_model_f_statistic,SpectrumScore-method get_model_f_statistic_p_value get_model_f_statistic_p_value,SpectrumScore-method get_model_residuals get_model_residuals,SpectrumScore-method get_model_slope get_model_slope,SpectrumScore-method plot,SpectrumScore,ANY-method plot,SpectrumScore-method show,SpectrumScore-method SpectrumScore-class |
| Subdivides Sequences into _n_ Bins | subdivide_data |
| Toy Motif Matrix | toy_motif_matrix |
