Files in broadinstitute/inferCNV
Infer Copy Number Variation from Single-Cell RNA-Seq Data
.Rbuildignore
.github/ISSUE_TEMPLATE/config.yml
.github/ISSUE_TEMPLATE/infercnv-support-and-development-hiatus.md
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
R/.wip/Seurat_integration.R
R/SplatterScrape.R
R/data.R
R/inferCNV.R
R/inferCNV_BayesNet.R
R/inferCNV_HMM.R
R/inferCNV_constants.R
R/inferCNV_heatmap.R
R/inferCNV_hidden_spike.R
R/inferCNV_i3HMM.R
R/inferCNV_mask_non_DE.R
R/inferCNV_meanVarSim.R
R/inferCNV_ops.R
R/inferCNV_simple_sim.R
R/inferCNV_tumor_subclusters.R
R/inferCNV_tumor_subclusters.random_smoothed_trees.R
R/infercnv_sampling.R
R/noise_reduction.R
R/seurat_interaction.R
README.md
Rstudio_helpers/Examine_and_Filter_Cells_and_Genes.Rmd
WDL/infercnv.wdl
data/HMM_states.rda
data/infercnv_annots_example.rda
data/infercnv_data_example.rda
data/infercnv_genes_example.rda
data/infercnv_object_example.rda
data/mcmc_obj.rda
docker/Dockerfile
example/Makefile
example/README.txt
example/__alt_exec_modes/run.no_spike.R
example/__alt_exec_modes/run.set_num_ref_groups.R
example/__alt_exec_modes/run.use_zscores.R
example/example.Rmd
example/run.R
example/run_memory_profiling_per_step.sh
example/run_test.R
inst/BUGS_Mixture_Model
inst/BUGS_Mixture_Model_i3
inst/CITATION
inst/NEWS
inst/extdata/gencode_downsampled.EXAMPLE_ONLY_DONT_REUSE.txt
inst/extdata/oligodendroglioma_annotations_downsampled.txt
inst/extdata/oligodendroglioma_expression_downsampled.counts.matrix.gz
inst/script/README.txt
man/CreateInfercnvObject.Rd
man/HMM_states.Rd
man/MCMC_inferCNV-class.Rd
man/add_to_seurat.Rd
man/apply_median_filtering.Rd
man/color.palette.Rd
man/filterHighPNormals.Rd
man/inferCNVBayesNet.Rd
man/infercnv-class.Rd
man/infercnv-package.Rd
man/infercnv_annots_example.Rd
man/infercnv_data_example.Rd
man/infercnv_genes_example.Rd
man/infercnv_object_example.Rd
man/mcmc_obj.Rd
man/plot_cnv.Rd
man/plot_per_group.Rd
man/plot_subclusters.Rd
man/run.Rd
man/sample_object.Rd
man/validate_infercnv_obj.Rd
scripts/ExploratoryPlots.R
scripts/HB_example_to_inferCNV_obj.R
scripts/KS_matrix_comparison.R
scripts/KS_matrix_comparison.use_infercnv_obj.R
scripts/QQ_matrix_comparison.R
scripts/apply_median_filtering.R
scripts/boxplot_cell_exprs.R
scripts/check_matrix_format.py
scripts/cross_cell_scaling_normalization.R
scripts/dropout_matrix_comparison.R
scripts/examine_dropout_logistic.R
scripts/examine_infercnv_data_params.R
scripts/examine_infercnv_data_params.just_dispersion.R
scripts/examine_normal_cutoffs_vs_KS.R
scripts/examine_normal_sampling_distributions.R
scripts/examine_normal_sampling_distributions.i3.R
scripts/examine_simulated_vs_observed_dispersion.R
scripts/examine_simulated_vs_observed_dispersion.from_matrix.R
scripts/explore_HMM_exec.R
scripts/explore_HMM_exec.hspike.R
scripts/explore_steps_by_gene.simple.R
scripts/genome_smoothed_lineplots.R
scripts/gtf_to_position_file.py
scripts/inferCNV.R
scripts/inferCNV_to_HB.R
scripts/inferCNV_utils.R
scripts/infercnv_obj_to_input_files.R
scripts/infercnv_validate.R
scripts/meanvar_sim_counts.R
scripts/plot_hspike.R
scripts/plot_hspike.by_num_cells.R
scripts/plot_hspike.diff_normal_tumor.R
scripts/plot_hspike_vs_sample_chrs.R
scripts/plot_infercnv_obj.R
scripts/plot_tumor_vs_normal_chr_densities.R
scripts/plot_tumor_vs_normal_chr_densities.i3.R
scripts/prepare_sparsematrix.R
scripts/recursive_random_tree_height_cutting.random_trees.R
scripts/recursive_random_tree_height_cutting.sigclust2.R
scripts/recursive_random_tree_height_cutting.using_hmms.R
scripts/run.stub.R
scripts/run_BayesNet.R
scripts/run_HMM_each_cell_separately.R
scripts/run_HMM_on_hspike.R
scripts/run_HMM_on_subclusters.R
scripts/run_HMM_per_chr.R
scripts/run_tests_sampling_and_group_plots.R
scripts/sim_vs_orig_counts.QQplot.R
scripts/splatterScrape_sim_counts.R
tests/testthat.R
tests/testthat/test_infer_cnv.R
vignettes/.wip/inferCNV.Rmd
vignettes/inferCNV.Rmd
