Package: transite 1.31.0

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:Konstantin Krismer [aut, cre, cph], Anna Gattinger [aut], Michael Yaffe [ths, cph], Ian Cannell [ths]

transite_1.31.0.tar.gz
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transite_1.31.0.tgz(r-4.5-x86_64)transite_1.31.0.tgz(r-4.5-arm64)
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transite_1.31.0.tgz(r-4.5-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
transite/json (API)

# Install 'transite' in R:

install.packages('transite', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

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-1.31.0(bioc 3.24)transite-1.30.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

geneexpression transcription differentialexpression microarray mrnamicroarray genetics genesetenrichment cpp

4.35 score 15 scripts 55 exports 38 dependencies

Last updated from:840af6551d. Checks:4 NOTE, 6 WARNING, 1 OK, 3 FAIL. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	186
linux-devel-arm64	WARNING	436
linux-devel-x86_64	WARNING	530
source / vignettes	OK	221
linux-release-arm64	WARNING	454
linux-release-x86_64	WARNING	530
macos-release-arm64	FAIL	71
macos-release-x86_64	FAIL	193
macos-oldrel-arm64	NOTE	472
macos-oldrel-x86_64	NOTE	797
windows-devel	WARNING	467
windows-release	WARNING	496
windows-oldrel	NOTE	489
wasm-release	FAIL	150

Exports:calculate_kmer_enrichment calculate_local_consistency calculate_motif_enrichment calculate_transcript_mc check_kmers classify_spectrum compute_kmer_enrichment create_kmer_motif create_kmer_origin_list create_matrix_motif draw_volcano_plot estimate_significance estimate_significance_core generate_iupac_by_kmers generate_iupac_by_matrix generate_kmers generate_kmers_from_iupac generate_permuted_enrichments geometric_mean get_adj_r_squared get_consistency_score get_consistency_score_n get_consistency_score_p_value get_heptamers get_hexamers get_id get_iupac get_model_degree get_model_f_statistic get_model_f_statistic_p_value get_model_residuals get_model_slope get_motif_by_id get_motif_by_rbp get_motif_matrix get_motifs get_motifs_meta_info get_ppm get_rbps get_source get_species get_type get_width init_iupac_lookup_table p_combine plot run_kmer_spma run_kmer_tsma run_matrix_spma run_matrix_tsma score_sequences score_spectrum score_transcripts set_motifs subdivide_data

Dependencies:BiocGenerics Biostrings cli cpp11 crayon dplyr farver generics GenomicRanges ggplot2 glue gridExtra gtable IRanges isoband labeling lifecycle magrittr pillar pkgconfig R6 RColorBrewer Rcpp rlang S4Vectors S7 scales Seqinfo stringi stringr TFMPvalue tibble tidyselect utf8 vctrs viridisLite withr XVector

Spectrum Motif Analysis (SPMA)

Analysis | Results | Additional information

Rendered fromspma.Rmdusingknitr::rmarkdown

Last update: 2020-08-25
Started: 2018-09-18

Citation

Development and contributors

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
Create _k_-mer lists with their original sequences	create_kmer_origin_list
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