Files in hesselberthlab/scrunchy
Single Cell Reconstruction of Functional Heterogeneity
.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
NEWS.md
R/RcppExports.R
R/clustering.R
R/data.R
R/dims.R
R/expt-haircut.R
R/expt.R
R/features.R
R/fsce.R
R/normalize.R
R/plots.R
R/reexport-colorblindr.R
R/scrunchy-package.R
R/stats.R
R/tidiers.R
R/utils-barcodes.R
R/utils.R
README.Rmd
README.md
codecov.yml
data-raw/.gitignore
data-raw/barcode_map_10x_v3.R
data-raw/fsce_small.R
data-raw/fsce_tidy.R
data-raw/human_gene_ids.R
data-raw/make_matrices.R
data/fsce_small.rda
data/fsce_tidy.rda
data/human_gene_ids.rda
inst/extdata/haircut/barcodes.tsv.gz
inst/extdata/haircut/features.tsv.gz
inst/extdata/haircut/matrix.mtx.gz
inst/extdata/mrna/barcodes.tsv.gz
inst/extdata/mrna/features.tsv.gz
inst/extdata/mrna/matrix.mtx.gz
man/FunctionalSingleCellExperiment-class.Rd
man/FunctionalSingleCellExperiment.Rd
man/add_label.Rd
man/add_stats.Rd
man/calc_cell_cycle.Rd
man/calc_hairpin_coverage.Rd
man/calc_pca.Rd
man/calc_qvalues.Rd
man/calc_tsne.Rd
man/calc_umap.Rd
man/calc_var_features.Rd
man/clr_normalize.Rd
man/cluster_kmeans.Rd
man/cluster_leiden.Rd
man/create_fsce.Rd
man/create_sce_feature.Rd
man/create_sce_haircut.Rd
man/create_sce_rnaseq.Rd
man/figures/README-activity_plot-1.png
man/figures/README-mrna_plot-1.png
man/figures/logo.png
man/filter_matrix.Rd
man/filter_molecules.Rd
man/fsce_small.Rd
man/fsce_tidy.Rd
man/human_gene_ids.Rd
man/is.molecule_df.Rd
man/log_normalize.Rd
man/molecule_df.Rd
man/normalize.Rd
man/palette_OkabeIto.Rd
man/pbmc_marker_genes.Rd
man/plot_activity.Rd
man/plot_barcodes.Rd
man/plot_dims.Rd
man/plot_dims_multi.Rd
man/plot_hairpin_coverage.Rd
man/plot_heatmap.Rd
man/plot_pcvariance.Rd
man/plot_saturation.Rd
man/read_matrix.Rd
man/read_molecules.Rd
man/scale_OkabeIto.Rd
man/scrunchy.Rd
man/scrunchy_data.Rd
man/stat_activity_grouped.Rd
man/stat_anova_grouped.Rd
man/stat_anova_tukey.Rd
man/tidy_all.Rd
man/tidy_coldata.Rd
man/tidy_counts.Rd
man/tidy_dims.Rd
man/tidy_logcounts.Rd
man/tidy_stats_grouped.Rd
man/umitools_to_mtx.Rd
man/write_matrix.Rd
pkgdown/_pkgdown.yml
pkgdown/extra.css
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
scrunchy.Rproj
src/.gitignore
src/Makevars
src/RcppExports.cpp
src/init.c
src/snn.cpp
tests/testthat.R
tests/testthat/test-calcs.R
tests/testthat/test-classes.R
tests/testthat/test-clustering.R
tests/testthat/test-dims.R
tests/testthat/test-io.R
tests/testthat/test-normalize.R
tests/testthat/test-plots.R
tests/testthat/test-stats.R
tests/testthat/test-tidiers.R
vignettes/.gitignore
vignettes/figures/method-overview.svg
vignettes/scrunchy.Rmd
