dravishays/scandal
A framework for single-cell analysis

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Functions
247
Source code
11
Man pages
51
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dravishays/scandal: A framework for single-cell analysis
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API

API for dravishays/scandal
A framework for single-cell analysis

Global functions
.W Source code
.aggregate_cell_ids Source code
.aggregate_gene_ids Source code
.assign_assay Source code
.assign_cna_score Source code
.assign_mps Source code
.bound_matrix Source code
.calc_cna_matrix Source code
.classify_cells Source code
.classify_cells_cluster_correlation Source code
.classify_cells_simple Source code
.classify_clusters Source code
.classify_intermediate_scores Source code
.classify_minc Source code
.classify_nimc Source code
.compute Source code
.compute_cor Source code
.compute_tsne Source code
.compute_umap Source code
.consensus_cluster Source code
.draw_grid Source code
.extract_programs Source code
.features Source code
.init_cell_class Source code
.is_option_requested Source code
.l2r Source code
.load_umi_matrix Source code
.mcs Source code
.metaprograms Source code
.mp_l2r Source code
.msg Source code
.nmf_matrix Source code
.plot_l2r_cor Source code
.prepare_cna_matrix Source code
.qc_stats Source code
.scandal_compute_cna_matrix Source code
.scandal_preprocess Source code
.score_mps Source code
.setup_data_dir Source code
.setup_plotting_dir Source code
.sparsity Source code
.subset_cells Source code
.valid_complexity_cutoff Source code
.valid_index Source code
DEFAULT_CELL_2_NODE_MAP Source code
DEFAULT_TITLE Source code
DefaultPreprocConfig Man page Source code
NODE_ID Source code
NucseqPreprocConfig Man page Source code
PROJ_ID Source code
PreprocConfig Man page Source code
PreprocConfig-class Man page
QCResults Man page Source code
QCResults-class Man page
SCANDAL_G1S_MARKERS Man page
SCANDAL_G2M_MARKERS Man page
SCANDAL_HOUSEKEEPING_GENES_LIST Man page
SCANDAL_IDH_A_AC_MARKERS Man page
SCANDAL_IDH_A_G1S_MARKERS Man page
SCANDAL_IDH_A_G2M_MARKERS Man page
SCANDAL_IDH_A_OC_MARKERS Man page
SCANDAL_IDH_A_STEMNESS_MARKERS Man page
SCANDAL_IDH_O_AC_MARKERS Man page
SCANDAL_IDH_O_G1S_MARKERS Man page
SCANDAL_IDH_O_G2M_MARKERS Man page
SCANDAL_IDH_O_OC_MARKERS Man page
SCANDAL_IDH_O_STEMNESS_MARKERS Man page
SCANDAL_MACROPHAGE_MARKERS Man page
SCANDAL_OLIGODENDROCYTE_MARKERS Man page
SS2PreprocConfig Man page Source code
ScandalDataSet Man page Source code
ScandalDataSet-class Man page
ScandalMetaprograms Source code
`%JCS%` Source code
`%MCD%` Source code
assign_metaprograms Source code
cell2SampleMap Man page
cell2SampleMap,ScandalDataSet-method Man page
cellIDs Man page
cellIDs,QCResults-method Man page
cellIDs<- Man page
cellIDs<-,QCResults-method Man page
center_matrix Man page Source code
cluster_variable_programs Source code
complexityCutoff Man page
complexityCutoff,PreprocConfig-method Man page
complexityCutoff<- Man page
complexityCutoff<-,PreprocConfig-method Man page
compute_complexity Man page Source code
compute_housekeeping Source code
compute_louvain_clusters Source code
compute_programs_sd Source code
count_genes_per_chromosome Source code
expressionCutoff Man page
expressionCutoff,PreprocConfig-method Man page
expressionCutoff<- Man page
expressionCutoff<-,PreprocConfig-method Man page
filter_low_housekeeping_cells Source code
filter_low_quality_cells Source code
filter_lowly_expressed_genes Source code
geneIDs Man page
geneIDs,QCResults-method Man page
geneIDs<- Man page
geneIDs<-,QCResults-method Man page
housekeepingCutoff Man page
housekeepingCutoff,PreprocConfig-method Man page
housekeepingCutoff<- Man page
housekeepingCutoff<-,PreprocConfig-method Man page
inspectSamples Man page
inspectSamples,ScandalDataSet-method Man page
is_config_object Source code
is_qc_results_object Source code
is_scandal_object Source code
is_valid_assay Source code
load_dataset Man page Source code
load_gene_pos_file Source code
logBase Man page
logBase,PreprocConfig-method Man page
logBase<- Man page
logBase<-,PreprocConfig-method Man page
log_transform Man page Source code
logtpm Man page
logtpm,ScandalDataSet-method Man page
logtpm<- Man page
logtpm<-,ScandalDataSet-method Man page
metaprograms Source code
nmf_extract_programs Source code
nmf_run Source code
nmf_score_genes Source code
nodeID Man page
nodeID,ScandalDataSet-method Man page
nodeID<- Man page
nodeID<-,ScandalDataSet-method Man page
prepare_nmf_matrix Source code
prepare_samples Source code
preprocConfig Man page
preprocConfig,QCResults-method Man page
preprocConfig,ScandalDataSet-method Man page
preprocess_matrix Man page Source code
projectID Man page
projectID,ScandalDataSet-method Man page
pseudoCount Man page
pseudoCount,PreprocConfig-method Man page
pseudoCount<- Man page
pseudoCount<-,PreprocConfig-method Man page
qualityControl Man page
qualityControl,ScandalDataSet-method Man page
qualityControl<- Man page
qualityControl<-,ScandalDataSet-method Man page
reverse_log_transform Man page Source code
sampleIDs Man page
sampleIDs,ScandalDataSet-method Man page
scalingFactor Man page
scalingFactor,PreprocConfig-method Man page
scalingFactor<- Man page
scalingFactor<-,PreprocConfig-method Man page
scandal Man page
scandal_cell_complexity_distribution_plot Man page Source code
scandal_cell_qc_data Source code
scandal_cluster_markers_density Man page Source code
scandal_cna_classify_cells Source code
scandal_cna_classify_scores Man page Source code
scandal_cna_compute_matrix Man page Source code
scandal_cna_compute_scores Man page Source code
scandal_cna_get_malignant_cells Source code
scandal_cna_infer Man page Source code
scandal_cna_plot Source code
scandal_cna_scores_plot Source code
scandal_complexity_distribution_plot Man page Source code
scandal_default_umap_config Source code
scandal_gene_qc_data Source code
scandal_histogram_plot Man page Source code
scandal_inspect_samples Man page Source code
scandal_load_data Man page Source code
scandal_markers_plot Source code
scandal_mean_expression_frequency_plot Man page Source code
scandal_mean_housekeeping_expression_plot Man page Source code
scandal_metaprograms Source code
scandal_plot Man page Source code
scandal_plot_qc_metrics Man page Source code
scandal_preprocess Man page Source code
scandal_program_clusters_plot Source code
scandal_programs_of_intra_sample_heterogeneity Man page Source code
scandal_programs_sd_plot Source code
scandal_quality_control_stats Man page Source code
scandal_reduced_dims_plot Man page Source code
scandal_save_data Man page Source code
scandal_scatter_plot Man page Source code
scandal_setup_analysis Man page Source code
scandal_simple_heatmap_plot Source code
scandal_tsne_plot Man page Source code
scandal_umap_plot Man page Source code
scandal_whiskers_plot Man page Source code
scat Source code
score_between_samples Source code
score_within_samples Source code
show,PreprocConfig-method Man page
show,QCResults-method Man page
show,ScandalDataSet-method Man page
statsQC Man page
statsQC,QCResults-method Man page
statsQC<- Man page
statsQC<-,QCResults-method Man page
typeMatrix Man page
typeMatrix,PreprocConfig-method Man page
typeMatrix<- Man page
typeMatrix<-,PreprocConfig-method Man page
umi2upm Source code
unprocessedData Man page
unprocessedData,ScandalDataSet-method Man page
within_sample_variable_programs Source code
dravishays/scandal documentation built on Jan. 8, 2020, 1:30 p.m.

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