Files in jmonlong/scCNAutils
Functions to analyze copy number aberrations in single-cell data

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
Makefile
NAMESPACE
R/RcppExports.R R/annotate_cna.R R/annotate_cna_seg.R R/auto_cna_call.R R/auto_cna_signal.R R/bin_genes.R R/call_cna.R R/call_cna_multisamps.R R/cnaHMM.R R/convert_to_coord.R R/define_cycling_cells.R R/find_communities.R R/gene_info.R R/make_metacells.R R/merge_samples.R R/metacells_cluster.R R/metacells_subsample.R R/norm_ge.R R/norm_ge_tmm.R R/norm_ge_total.R R/plot_aneuploidy.R R/plot_cna.R R/plot_communities.R R/plot_heatmap.R R/plot_qc_cells.R R/plot_tsne.R R/plot_umap.R R/qc_cells.R R/qc_filter.R R/read_mtx.R R/rebin_cov.R R/rm_cv_outliers.R R/run_louvain.R R/run_pca.R R/run_tsne.R R/run_umap.R R/scCNAutils.R R/smooth_movingw.R R/tsne_browser.R R/umap_browser.R R/winsor.R R/zscore.R README.md docs/README.md
docs/cell-cycle-genes-tirosh2016.tsv
docs/debug-hmm.R
docs/flowchart-cnacalling.mmd
docs/flowchart-cnacalling.png
docs/flowchart-cnasignal.mmd
docs/flowchart-cnasignal.png
docs/oligodendroglioma-analysis.R docs/scCNAutils-manual.pdf man/annotate_cna.Rd man/annotate_cna_seg.Rd man/auto_cna_call.Rd man/auto_cna_signal.Rd man/binGenesC.Rd man/bin_genes.Rd man/call_cna.Rd man/call_cna_multisamps.Rd man/cnaHMM.Rd man/convert_to_coord.Rd man/define_cycling_cells.Rd man/find_communities.Rd man/gene_info.Rd man/make_metacells.Rd man/merge_samples.Rd man/metacells_cluster.Rd man/metacells_subsample.Rd man/norm_ge.Rd man/norm_ge_tmm.Rd man/norm_ge_total.Rd man/plot_aneuploidy.Rd man/plot_cna.Rd man/plot_communities.Rd man/plot_heatmap.Rd man/plot_qc_cells.Rd man/plot_tsne.Rd man/plot_umap.Rd man/qc_cells.Rd man/qc_filter.Rd man/read_mtx.Rd man/rebin_cov.Rd man/rm_cv_outliers.Rd man/run_louvain.Rd man/run_pca.Rd man/run_tsne.Rd man/run_umap.Rd man/scCNAutils-package.Rd man/smoothMovingC.Rd man/smooth_movingw.Rd man/tmmNormC.Rd man/tsne_browser.Rd man/umap_browser.Rd man/winsor.Rd man/zscore.Rd
src/.gitignore
src/RcppExports.cpp
src/binGenes.cpp
src/smoothMovingC.cpp
src/tmmNorm.cpp
tests/testthat.R tests/testthat/test_aneuploidy.R tests/testthat/test_auto.R tests/testthat/test_bin.R tests/testthat/test_cna.R tests/testthat/test_community.R tests/testthat/test_coord.R tests/testthat/test_mergesamp.R tests/testthat/test_metacell.R tests/testthat/test_norm.R tests/testthat/test_pca.R tests/testthat/test_qc.R tests/testthat/test_read.R tests/testthat/test_rebincov.R tests/testthat/test_rmol.R tests/testthat/test_smooth.R tests/testthat/test_tsne.R tests/testthat/test_zscore.R
jmonlong/scCNAutils documentation built on June 13, 2019, 5:09 a.m.