Man pages for pcahan1/cancerCellNet
CellNet, for cancer
| addRandToSampTab | Add Random Profiles to Sample Table |
| aggregate_scProfiles | Aggregate scRNA Profiles |
| avgGeneCat | Average Category Gene Expressions |
| barPlotGene | Plot Specific Gene Expression |
| broadClass_predict | Predict query using broad class classifier |
| broadClass_train | Broad Class Training |
| calc_normTfScore | Calculate the TF normalization constant Calculate the TF... |
| calc_tfScores | Calculate the TF Calculate the TF score given all the... |
| ccn_classAssess | Assessment of Classifier |
| ccn_extractRegsDF | extracts the TRs, zscores, and corr values passing thresh |
| ccn_extract_SN_DF | returns a DF of: sample_id, description, ctt, subnet_name,... |
| ccn_findSpecGenes | find genes that are preferentially expressed in specified... |
| ccn_getRawGRN | get raw GRN from zscores, and corr |
| ccn_get_targets | get targets of a tf |
| ccn_hmClass | Heatmap of the classification result |
| ccn_makeGRN | make GRN |
| ccn_MakeTLs | get targets of tFs |
| ccn_make_tVals | Estimate gene expression dist in CTs |
| ccn_make_tVals_predict | ccn_make_tVals_predict |
| ccn_netScores | GRN status |
| ccn_normalizeScores | Normalize grn status as compared to training data |
| ccn_queryGRNstatus | Get Query GRN status |
| ccn_rawScore | computes the raw z score for a gene as xmax-abs(zscore). |
| ccn_reduceMatLarge | reduce large matrix reduce large matrix from... |
| ccn_sampR_to_pattern | return a pattern for use in ccn_testPattern (template... |
| ccn_score | GRN status |
| ccn_specGenesAll | finds general and context dependent specifc genes |
| ccn_specGRNs | extract sub-networks made up of CT genes; |
| ccn_testPattern | template matching |
| ccn_tfScores | calculate TF scores |
| ccn_trainNorm | Figure out normalization factors for GRNs, and norm training... |
| ccn_zscoreVect | Compute mean Z scores of given genes |
| cn_clPerf | run cn_clPerf across thresholds |
| cn_eval | determine performance of classification at given threshold |
| compareGenePairs | Compile genePairs comparison matrix |
| conversionList | List of Gene Conversion dataframe |
| downSampleW | Weighted subtraction from mapped reades |
| findBestPairs | Find best pairs |
| findClassyGenes | Find Classifier-Worthy Gene Candidates |
| find_tfs | find transcript factors |
| geneScores | score indvidual genes |
| getClassGenes | Find Classy Genes |
| gnrAll | Find Genes in Clusters compare to other categories |
| grn_corr_round | gene-gene correlations, and round |
| grn_zscores | compute CLR-like zscores |
| hm_gpa_sel | Heatmap of the genes and groups |
| ig_tabToIgraph | convert a table to an igraph |
| logRank | logRank gene expression |
| makeClassifier | Make Classifier |
| makeGeneCompareTab | Make Gene Comparison Table |
| makePairTab | Make the pair tabs |
| makeSubClassifier | Make Classifier tailored for subclassifier |
| mat_zscores | compute context dependent zscores |
| meanTraining | calculate the mean GRN scores across categories |
| minDif | Min Difference |
| ModifiedRandomize | Randomize the data matrix |
| parallel_quickPairs | function for parallel computation of quick pairs... |
| plot_class_PRs | Plot precision recall curve per category |
| plotGeneComparison | Gene expression plotting |
| processImportance | process classifier importance |
| ptGetTop | Find the best gene pairs for training |
| ptSmall | Pair Transform on small scale |
| query_transform | Make complete gene-to-gene comparison |
| randomize | Randomize the data matrix |
| rf_classPredict | Classify Query Samples |
| sc_compAlpha | Compute Alpha |
| sc_compMu | compute Mu |
| sc_cov | Compute Coefficient of Variation |
| sc_fano | Compute Fano Factor |
| sc_filterGenes | Find Genes that Pass Criteria |
| sc_sampR_to_pattern | Create Template |
| sc_statTab | Generate a Stats Table |
| sc_testPattern | Template Matching |
| sdGeneCat | Standard Deviation Category Gene Expressions |
| splitCommon | Split Sample Table |
| splitCommon_proportion | Split training set and validation set |
| subClass_predict | Predict sub class query using broad class and subclass... |
| subClassQuery_transform | Sub-class Query Transform |
| subClass_train | Sub-Class Training (new and improved version) with merged... |
| trans_prop | Log scaled downsampled expression |
| utils_convertToGeneSymbols | Gene Symbol Conversion |
| utils_loadObject | Load an R object |
| utils_matchSampTab | Match Sample Table |
| utils_reduceMat | Reduce data matrix |
| weighted_down | Down Sample Gene Expressions |
| zscore | Z scores Figure out Z score given mean and standard deviation |
