Package index • SeedMatchR

All functions

SeedMatchR(): Find seed matches in genomic features

SeedMatchReport(): Generate statistics based on sequence matches and DE data

as_dataframe_mp_matches(): as_dataframe_mp_matches

benchmark_preds(): Benchmark seed match predictions

build_annotation_filter(): Build an AnnotationFilter::AnnotationFilter for selecting transcripts

check_bulges_nt(): check_bulges_nt

create_graph(): Create a graph of protein-protein interactions from stringDB

deseq_fc_ecdf(): Plot the ECDF of log2(fold change) between groups

.check_gene_list_overlap(): Check if input gene lists overlap

.create_alignment_df(): Create a dataframe of alignment information

.find_factorial_internal(): find_factorial_internal

.gc_content(): .gc_content

.get_all_combination_w_b(): get_all_combination_w_b

.get_canonical_seed(): Get the target sequence for canonical seed definitions

.get_counts_column(): Get match results as a column of counts appended to a differential expression results data.frame

.get_custom_sequence(): Get a custom target sequence based on start and stop position

.get_longest_utr(): Get the longest transcript per gene

.get_match_df(): Get sequence matches as a data.frame

.get_target_bulged_guides(): get_target_bulged_guides

.make_space(): Create a vector of spaces for padding sequences for alignment

.matchStrings(): Match two strings of the same size and return a character vector to represent positions that match

.plot_ecdf(): Use ggplot2 to plot the ecdf for log2 fold changes

.reduce_features(): Reduce 3' UTRs to the gene level across all transcripts

.sequence_with_tb(): .sequence_with_tb

.update_sequence_at(): .update_sequence_at

download_parse_file(): Download and parse DESeq2 output from GSE184929

ecdf_stat_test(): Test for differences in log2(Fold Change) ECDFs between two gene lists

filter_res(): Filter differential expression results

full_search(): Search input Biostrings::DNAStringSet for a set of defined sequences

full_search_ranges(): Search input Biostrings::DNAStringSet for a set of defined sequences

generate_e_value(): generate_e_value

get_3UTR_granges(): Extract GenomicRanges::GRangesList of 3' UTRs

get_compensatory_sequences(): get_compensatory_sequences

get_example_data(): Download example DESeq2 data from GEO

get_network_matches(): get_network_matches

get_seed(): Get the target sequence for a given siRNA input sequence

get_stringPPI_to_stringGGI(): get_stringPPI_to_stringGGI

kmer_hist(): Plot a histogram of kmer frequency across genes

load_annotations(): Load species-specific annotations needed to run SeedMatchR()

load_example_data(): Load example DESeq2 data into the environment

load_species_anno_db(): Load species-specific annotations from AnnotationHub

match_distances(): Find inter match distances for each gene

message_passing(): message_passing

plotAlignment(): Plot matches as alignments against target sequence feature

run_wobble_bulges_pipeline(): Running wobble and bulge inclusive seedmatchR pipeline

sequence_kmer_counts(): Count the k-mer frequency in a set of sequences

vmatchPattern2(): A modified vmatchPattern function that supports indels and mismatches

wass_dist(): Function to compute overall, positive, and negative Wasserstein differences between ECDFs