Man pages for Sage-Bionetworks/sageseqr
Identify differentially expressed genes counts data
| association_statistic_for_factors | Compute the association statistic for factor variables |
| association_statistics_for_both | Find intraclass correlation (ICC) between factor and... |
| biomart_obj | Get available Ensembl dataset |
| biomart_stats | Get Gene Length and GC: biomart |
| boxplot_vars | Explore metadata by variable. |
| build_formula | Formula Builder |
| check_mismatch | Check for consistent identifiers |
| clean_covariates | Create covariate matrix from tidy metadata data frame. |
| coerce_continuous | Coerce objects to type numeric. |
| coerce_factors | Coerce objects to type factors. |
| collapse_duplicate_hgnc_symbol | Duplicate HGNC |
| complete_path | Create complete URL to Synapse entity |
| compute_residuals | Compute residualized counts matrix |
| conditional_plot_sexcheck | Conditionally wrap plot_sexcheck for targets |
| convert_geneids | Get gene Ids |
| correlate_and_plot | Calculate correlation between covariates and principal... |
| cqn | Conditional Quantile Normalization (CQN) |
| differential_expression | Differential Expression with Dream |
| dropped_genes | Dropped Genes Finder |
| filter_genes | Filter genes |
| get_association_statistics | Visualize relationship between variables |
| get_biomart | Get Ensembl biomaRt object |
| get_data | Detect file type and download data |
| gtf_stats | Get Gene Length and GC: GTF/Fasta |
| identify_outliers | Explore samples that are outliers |
| parse_counts | Subset counts data frame |
| plot_coexpression | Co-expression histogram generation |
| plot_pcs_with_covariates | Explore relationship between principal components (PCs) and... |
| plot_sexcheck | Explore metadata by gene expression on the sex chromosomes. |
| plot_sexcheck_pca | Explore metadata by gene expression on the sex chromosomes... |
| plot_volcano | Volcano plot differential expression results' |
| prepare_results | Prepare output |
| provenance_helper | Provenance helper |
| reexports | Objects exported from other packages |
| run_pca | Principal Component Analysis (PCA) of samples |
| run_pca_and_plot_correlations | Compute principal component analysis (PCA) and plot... |
| simple_filter | Filter genes with low expression |
| start_de | Initialize differential expression analysis workflow |
| stepwise_regression | Stepwise Regression |
| store_results | Store output to Synapse |
| summarize_biotypes | Summarize Biotypes |
| threshold_fdr | Apply false discovery rate (FDR) threshold to correlation... |
| wrap_de | Wrapper for Differential Expression Analysis |
