Files in jhammelman/spatzie
Identification of enriched motif pairs from chromatin interaction data
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE.md
NAMESPACE
NEWS
R/anchor_pair_enrich.R
R/compare_motif_pairs.R
R/data.R
R/filter_motifs.R
R/filter_pair_motifs.R
R/find_ep_coenrichment.R
R/get_specific_interactions.R
R/plot_motif_occurrence.R
R/scan_motifs.R
R/zzz.R
README.md
data-raw/41586_2020_2151_MOESM5_ESM.bedpe.txt.gz
data-raw/prepare_human_examples.R
data-raw/prepare_mouse_examples.R
data-raw/process_test_examples.R
data/anchor_pair_example_count.rda
data/anchor_pair_example_match.rda
data/anchor_pair_example_score.rda
data/compare_pairs_example.rda
data/filter_pairs_example.rda
data/int_data_k562.rda
data/int_data_mslcl.rda
data/int_data_yy1.rda
data/interactions_yy1.rda
data/interactions_yy1_enhancer.rda
data/interactions_yy1_ep.rda
data/interactions_yy1_promoter.rda
data/scan_interactions_example.rda
data/scan_interactions_example_filtered.rda
inst/CITATION
inst/extdata/HOCOMOCOv11_core_HUMAN_mono.txt.gz
inst/extdata/HOCOMOCOv11_core_MOUSE_mono.txt.gz
inst/extdata/motifs_subset.txt.gz
inst/extdata/yy1_interactions.bedpe.gz
man/anchor_pair_enrich.Rd
man/anchor_pair_example_count.Rd
man/anchor_pair_example_match.Rd
man/anchor_pair_example_score.Rd
man/compare_motif_pairs.Rd
man/compare_pairs_example.Rd
man/filter_motifs.Rd
man/filter_pair_motifs.Rd
man/filter_pairs_example.Rd
man/find_ep_coenrichment.Rd
man/get_specific_interactions.Rd
man/int_data_k562.Rd
man/int_data_mslcl.Rd
man/int_data_yy1.Rd
man/interactions_yy1.Rd
man/interactions_yy1_enhancer.Rd
man/interactions_yy1_ep.Rd
man/interactions_yy1_promoter.Rd
man/plot_motif_occurrence.Rd
man/scan_interactions_example.Rd
man/scan_interactions_example_filtered.Rd
man/scan_motifs.Rd
man/spatzie.Rd
tests/testthat.R
tests/testthat/test_anchor_pair.R
tests/testthat/test_filter.R
tests/testthat/test_helpers.R
tests/testthat/test_pair_filter.R
tests/testthat/test_plotting.R
tests/testthat/test_scan.R
vignettes/bibliography.bib
vignettes/figure/is_annotate_interactions-1.png
vignettes/figure/is_compute_cosignificance_count-1.png
vignettes/figure/is_compute_cosignificance_score-1.png
vignettes/figure/sc_annotate_interactions-1.png
vignettes/figure/sc_compute_cosignificance_count-1.png
vignettes/individual-steps.Rmd
vignettes/individual-steps.Rmd.orig
vignettes/precompile.R
vignettes/single-call.Rmd
vignettes/single-call.Rmd.orig
