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
data-natcom2020/README.md
data-natcom2020/cells-community-normal-natcom2020.tsv.gz
data-natcom2020/conv.R
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
