Find Matches to Canonical SiRNA Seeds in Genomic Features


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Documentation for package ‘SeedMatchR’ version 1.0.1

Help Pages

check_gene_list_overlap Check if input gene lists overlap
deseq_fc_ecdf Plot the ecdf for DESeq2 log2 Fold Changes
download_parse_file Download and parse DESeq2 output from GSE184929
dstat_histogram Plot a histogram of dstat statistics from tests provided by the 'twosamples' package
ecdf_stat_test Test for differences in log2(Fold Change) ECDFs between two gene lists using the 'twosamples' package
filter_deseq Filter DESEQ2 Results for SeedMatchR
generate_possible_seqs Generate all possible sequence permutations given an alphabet and length
get_example_data Download example DESeq2 data from GEO
get_feature_seqs Get transcripts features and feature sequences
get_seed Get the target seed sequence given a canonical seed name and input sequence
load_example_data Load example DESeq2 data into the environment
load_species_anno_db Load species specific 'AnnotationDb'
plot_seeds Plot the Guide Strand with different optional seeds
SeedMatchR Find seed matches in genomic features