Files in cole-trapnell-lab/cicero
Predict cis-co-accessibility from single-cell chromatin accessibility data
.Rbuildignore
.github/.gitignore
.github/workflows/check-standard.yaml
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/activityScores.R
R/aggregate.R
R/cicero.R
R/data.R
R/fromGviz.R
R/plotting.R
R/runCicero.R
R/utils.R
README.md
code-of-conduct.md
codecov.yml
data/cell_data.rda
data/cicero_data.rda
data/gene_annotation_sample.rda
data/human.hg19.genome.rda
inst/CITATION
man/aggregate_by_cell_bin.Rd
man/aggregate_nearby_peaks.Rd
man/annotate_cds_by_site.Rd
man/assemble_connections.Rd
man/build_gene_activity_matrix.Rd
man/cell_data.Rd
man/cicero-package.Rd
man/cicero_data.Rd
man/compare_connections.Rd
man/df_for_coords.Rd
man/estimate_distance_parameter.Rd
man/find_overlapping_ccans.Rd
man/find_overlapping_coordinates.Rd
man/gene_annotation_sample.Rd
man/generate_ccans.Rd
man/generate_cicero_models.Rd
man/human.hg19.genome.Rd
man/make_atac_cds.Rd
man/make_cicero_cds.Rd
man/make_sparse_matrix.Rd
man/normalize_gene_activities.Rd
man/plot_accessibility_in_pseudotime.Rd
man/plot_connections.Rd
man/ranges_for_coords.Rd
man/run_cicero.Rd
tests/cicero_data_sub.txt
tests/feat.txt
tests/feat_head.txt
tests/figs/deps.txt
tests/figs/plotting/basic-bar-high-breaks.svg
tests/figs/plotting/basic-bar-one.svg
tests/figs/plotting/basic-bar.svg
tests/figs/plotting/basic-connections-all-bp.svg
tests/figs/plotting/basic-connections-chr-bp1.svg
tests/figs/plotting/basic-connections-chr.svg
tests/figs/plotting/basic-connections-comparison-plot.svg
tests/figs/plotting/basic-connections-high-comparison-cutoff.svg
tests/figs/plotting/basic-connections-high-cutoff.svg
tests/figs/plotting/basic-connections-include-axis-track.svg
tests/figs/plotting/basic-connections-plot-bad-chr.svg
tests/figs/plotting/basic-connections-plot-comparison-cutoff.svg
tests/figs/plotting/basic-connections-plot-cutoff.svg
tests/figs/plotting/basic-connections-plot-dt.svg
tests/figs/plotting/basic-connections-plot-with-viewpoint-change-colors.svg
tests/figs/plotting/basic-connections-plot-with-viewpoint-no-comp.svg
tests/figs/plotting/basic-connections-plot-with-viewpoint.svg
tests/figs/plotting/basic-connections-plot.svg
tests/figs/plotting/comparison-connection-color-color-column.svg
tests/figs/plotting/comparison-connection-color-comparison-connection-width.svg
tests/figs/plotting/comparison-connection-color-type-column-coaccess-no-legend.svg
tests/figs/plotting/comparison-connection-color-type-column-coaccess.svg
tests/figs/plotting/comparison-connection-color-type-column.svg
tests/figs/plotting/comparison-connection-color.svg
tests/figs/plotting/comparison-peak-color-color-column.svg
tests/figs/plotting/comparison-peak-color-logical-column.svg
tests/figs/plotting/comparison-peak-color-type-column.svg
tests/figs/plotting/comparison-peak-color.svg
tests/figs/plotting/comparison-ymax-plus-cutoff.svg
tests/figs/plotting/comparison-ymax.svg
tests/figs/plotting/connection-color-color-column.svg
tests/figs/plotting/connection-color-connection-width.svg
tests/figs/plotting/connection-color-type-column-coaccess-no-legend.svg
tests/figs/plotting/connection-color-type-column-coaccess.svg
tests/figs/plotting/connection-color-type-column.svg
tests/figs/plotting/connection-color.svg
tests/figs/plotting/connection-ymax-plus-cutoff.svg
tests/figs/plotting/connection-ymax.svg
tests/figs/plotting/connections-plot-with-collapsetranscripts-gene.svg
tests/figs/plotting/connections-plot-with-collapsetranscripts-longest.svg
tests/figs/plotting/connections-plot-with-collapsetranscripts-meta.svg
tests/figs/plotting/connections-plot-with-collapsetranscripts-shortest.svg
tests/figs/plotting/connections-plot-with-collapsetranscripts-true.svg
tests/figs/plotting/connections-plot-with-comparison-color.svg
tests/figs/plotting/connections-plot-with-comparison-peak-color-hex.svg
tests/figs/plotting/connections-plot-with-comparison-peak-color.svg
tests/figs/plotting/connections-plot-with-comparison.svg
tests/figs/plotting/connections-plot-with-gene-model-color.svg
tests/figs/plotting/connections-plot-with-gene-model-no-genes.svg
tests/figs/plotting/connections-plot-with-gene-model-with-comparison.svg
tests/figs/plotting/connections-plot-with-gene-model.svg
tests/figs/plotting/peak-color-color-column.svg
tests/figs/plotting/peak-color-logical-column.svg
tests/figs/plotting/peak-color-type-column.svg
tests/figs/plotting/peak-color.svg
tests/human.hg19.genome_sub.txt
tests/testthat.R
tests/testthat/_snaps/plotting/basic-bar-high-breaks.svg
tests/testthat/_snaps/plotting/basic-bar-one.svg
tests/testthat/_snaps/plotting/basic-bar.svg
tests/testthat/_snaps/plotting/basic-connections-all-bp.svg
tests/testthat/_snaps/plotting/basic-connections-chr-bp1.svg
tests/testthat/_snaps/plotting/basic-connections-chr.svg
tests/testthat/_snaps/plotting/basic-connections-comparison-plot.svg
tests/testthat/_snaps/plotting/basic-connections-high-comparison-cutoff.svg
tests/testthat/_snaps/plotting/basic-connections-high-cutoff.svg
tests/testthat/_snaps/plotting/basic-connections-include-axis-track.svg
tests/testthat/_snaps/plotting/basic-connections-plot-bad-chr.svg
tests/testthat/_snaps/plotting/basic-connections-plot-comparison-cutoff.svg
tests/testthat/_snaps/plotting/basic-connections-plot-cutoff.svg
tests/testthat/_snaps/plotting/basic-connections-plot-dt.svg
tests/testthat/_snaps/plotting/basic-connections-plot-with-viewpoint-change-colors.svg
tests/testthat/_snaps/plotting/basic-connections-plot-with-viewpoint-no-comp.svg
tests/testthat/_snaps/plotting/basic-connections-plot-with-viewpoint.svg
tests/testthat/_snaps/plotting/basic-connections-plot.svg
tests/testthat/_snaps/plotting/comparison-connection-color-color-column.svg
tests/testthat/_snaps/plotting/comparison-connection-color-comparison-connection-width.svg
tests/testthat/_snaps/plotting/comparison-connection-color-type-column-coaccess-no-legend.svg
tests/testthat/_snaps/plotting/comparison-connection-color-type-column-coaccess.svg
tests/testthat/_snaps/plotting/comparison-connection-color-type-column.svg
tests/testthat/_snaps/plotting/comparison-connection-color.svg
tests/testthat/_snaps/plotting/comparison-peak-color-color-column.svg
tests/testthat/_snaps/plotting/comparison-peak-color-logical-column.svg
tests/testthat/_snaps/plotting/comparison-peak-color-type-column.svg
tests/testthat/_snaps/plotting/comparison-peak-color.svg
tests/testthat/_snaps/plotting/comparison-ymax-plus-cutoff.svg
tests/testthat/_snaps/plotting/comparison-ymax.svg
tests/testthat/_snaps/plotting/connection-color-color-column.svg
tests/testthat/_snaps/plotting/connection-color-connection-width.svg
tests/testthat/_snaps/plotting/connection-color-type-column-coaccess-no-legend.svg
tests/testthat/_snaps/plotting/connection-color-type-column-coaccess.svg
tests/testthat/_snaps/plotting/connection-color-type-column.svg
tests/testthat/_snaps/plotting/connection-color.svg
tests/testthat/_snaps/plotting/connection-ymax-plus-cutoff.svg
tests/testthat/_snaps/plotting/connection-ymax.svg
tests/testthat/_snaps/plotting/connections-plot-with-collapsetranscripts-gene.svg
tests/testthat/_snaps/plotting/connections-plot-with-collapsetranscripts-longest.svg
tests/testthat/_snaps/plotting/connections-plot-with-collapsetranscripts-meta.svg
tests/testthat/_snaps/plotting/connections-plot-with-collapsetranscripts-shortest.svg
tests/testthat/_snaps/plotting/connections-plot-with-collapsetranscripts-true.svg
tests/testthat/_snaps/plotting/connections-plot-with-comparison-color.svg
tests/testthat/_snaps/plotting/connections-plot-with-comparison-peak-color-hex.svg
tests/testthat/_snaps/plotting/connections-plot-with-comparison-peak-color.svg
tests/testthat/_snaps/plotting/connections-plot-with-comparison.svg
tests/testthat/_snaps/plotting/connections-plot-with-gene-model-color.svg
tests/testthat/_snaps/plotting/connections-plot-with-gene-model-no-genes.svg
tests/testthat/_snaps/plotting/connections-plot-with-gene-model-with-comparison.svg
tests/testthat/_snaps/plotting/connections-plot-with-gene-model.svg
tests/testthat/_snaps/plotting/peak-color-color-column.svg
tests/testthat/_snaps/plotting/peak-color-logical-column.svg
tests/testthat/_snaps/plotting/peak-color-type-column.svg
tests/testthat/_snaps/plotting/peak-color.svg
tests/testthat/test-aggregate.R
tests/testthat/test-plotting.R
tests/testthat/test-runCicero.R
tests/testthat/test-utils.R
tests/tsne_coord.Rdata
vignettes/website.Rmd
