Files in broadinstitute/infercnv

Infer Copy Number Variation from Single-Cell RNA-Seq Data

.Rbuildignore

.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

broadinstitute/infercnv documentation built on Dec. 3, 2023, 6:58 p.m.