Files in cicero
Precict cis-co-accessibility from single-cell chromatin accessibility data

NEWS
LICENSE
DESCRIPTION
README.md
NAMESPACE
inst/CITATION
inst/doc/website.R
inst/doc/website.html
inst/doc/website.Rmd vignettes/website.Rmd R/runCicero.R R/data.R R/plotting.R R/fromGviz.R R/utils.R R/activityScores.R R/aggregate.R R/cicero.R man/cell_data.Rd man/cicero-package.Rd man/df_for_coords.Rd man/compare_connections.Rd man/aggregate_nearby_peaks.Rd man/estimate_distance_parameter.Rd man/gene_annotation_sample.Rd man/generate_ccans.Rd man/find_overlapping_ccans.Rd man/annotate_cds_by_site.Rd man/cicero_data.Rd man/plot_connections.Rd man/run_cicero.Rd man/plot_accessibility_in_pseudotime.Rd man/make_atac_cds.Rd man/build_gene_activity_matrix.Rd man/normalize_gene_activities.Rd man/make_cicero_cds.Rd man/human.hg19.genome.Rd man/ranges_for_coords.Rd man/assemble_connections.Rd man/find_overlapping_coordinates.Rd man/aggregate_by_cell_bin.Rd man/make_sparse_matrix.Rd man/generate_cicero_models.Rd
build/vignette.rds
tests/tsne_coord.Rdata
tests/testthat.R
tests/feat.txt
tests/cicero_data_sub.txt
tests/feat_head.txt
tests/human.hg19.genome_sub.txt
tests/testthat/test-plotting.R tests/testthat/test-aggregate.R tests/testthat/test-utils.R tests/testthat/test-runCicero.R
tests/figs/deps.txt
tests/figs/plotting/connections-plot-with-gene-model-with-comparison.svg
tests/figs/plotting/connection-color-type-column-coaccess.svg
tests/figs/plotting/comparison-connection-color-type-column-coaccess.svg
tests/figs/plotting/connections-plot-with-collapsetranscripts-true.svg
tests/figs/plotting/basic-connections-plot-with-viewpoint-change-colors.svg
tests/figs/plotting/peak-color-type-column.svg
tests/figs/plotting/basic-bar.svg
tests/figs/plotting/comparison-connection-color-type-column.svg
tests/figs/plotting/connection-color.svg
tests/figs/plotting/connections-plot-with-gene-model-no-genes.svg
tests/figs/plotting/comparison-peak-color-type-column.svg
tests/figs/plotting/connection-color-color-column.svg
tests/figs/plotting/basic-connections-plot-with-viewpoint.svg
tests/figs/plotting/connection-color-type-column-coaccess-no-legend.svg
tests/figs/plotting/peak-color.svg
tests/figs/plotting/basic-connections-chr.svg
tests/figs/plotting/connection-color-type-column.svg
tests/figs/plotting/basic-connections-all-bp.svg
tests/figs/plotting/basic-connections-high-cutoff.svg
tests/figs/plotting/basic-connections-include-axis-track.svg
tests/figs/plotting/connections-plot-with-collapsetranscripts-longest.svg
tests/figs/plotting/comparison-peak-color-color-column.svg
tests/figs/plotting/basic-connections-comparison-plot.svg
tests/figs/plotting/connection-color-connection-width.svg
tests/figs/plotting/connections-plot-with-comparison-peak-color.svg
tests/figs/plotting/connection-ymax-plus-cutoff.svg
tests/figs/plotting/comparison-connection-color-comparison-connection-width.svg
tests/figs/plotting/peak-color-color-column.svg
tests/figs/plotting/basic-connections-high-comparison-cutoff.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.svg
tests/figs/plotting/comparison-connection-color-type-column-coaccess-no-legend.svg
tests/figs/plotting/basic-connections-plot-with-viewpoint-no-comp.svg
tests/figs/plotting/basic-connections-plot.svg
tests/figs/plotting/comparison-ymax.svg
tests/figs/plotting/basic-connections-plot-comparison-cutoff.svg
tests/figs/plotting/basic-connections-plot-cutoff.svg
tests/figs/plotting/connections-plot-with-collapsetranscripts-meta.svg
tests/figs/plotting/comparison-connection-color.svg
tests/figs/plotting/connections-plot-with-gene-model.svg
tests/figs/plotting/connection-ymax.svg
tests/figs/plotting/basic-bar-high-breaks.svg
tests/figs/plotting/comparison-connection-color-color-column.svg
tests/figs/plotting/peak-color-logical-column.svg
tests/figs/plotting/connections-plot-with-collapsetranscripts-gene.svg
tests/figs/plotting/connections-plot-with-collapsetranscripts-shortest.svg
tests/figs/plotting/comparison-ymax-plus-cutoff.svg
tests/figs/plotting/comparison-peak-color-logical-column.svg
tests/figs/plotting/comparison-peak-color.svg
tests/figs/plotting/connections-plot-with-gene-model-color.svg
tests/figs/plotting/basic-connections-chr-bp1.svg
tests/figs/plotting/basic-bar-one.svg
data/cell_data.rda
data/cicero_data.rda
data/human.hg19.genome.rda
data/gene_annotation_sample.rda
cicero documentation built on Feb. 22, 2019, 2:01 a.m.