Man pages for HuntsmanCancerInstitute/hciR
RNA-seq workflows at HCI
| annotate_results | Annotate DESeq2 results |
| as_matrix | Convert tibbles to a matrix |
| check_contrasts | Check contrasts |
| deseq_from_tibble | Run DESeq from tibbles |
| extract_samples | Parse sample from file names |
| fgsea_all | Run fgsea on all DESeq2 result tables |
| filter_counts | Filter count matrix |
| filter_top_counts | Filter top count matrix |
| gdc_coldata | GDC column data |
| gdc_rowdata | GDC row data |
| gene_intersect | Compare genes to sets |
| palette255 | Expand RColorBrewer palettes |
| pasilla | DESeq objects and results for Pasilla knock-downs |
| plot_biotypes | Plot reads assigned to biotypes |
| plot_counts | Plot counts for a single gene |
| plot_dist | Plot heatmap of sample distances |
| plot_fgsea | Plot fGSEA output |
| plot_filter | Plot count matrix to check filter cutoff |
| plot_genes | Plot heatmap of top genes |
| plot_interactions | Plot counts for many genes |
| plot_ma | Highchart version of MA-plot |
| plot_pca | Highchart version of plotPCA in DESeq2 |
| plot_volcano | Volcano plot |
| print_genes | Print the scaled values from plot_genes and optionally add... |
| read_biomart | Read biomart annotations |
| read_deseq | Read a DESeq Excel file from write_deseq |
| read_featureCounts | Read featureCounts output files |
| read_gsea | Read GSEA enrichment files |
| read_idxstats | Read samtools idxstats output |
| read_ipa | Read IPA Expression Analysis |
| read_RnaSeqMetrics | Read CollectRnaSeqMetrics output |
| read_RSEM | Read RSEM output files |
| read_sample_files | Read and combine common output files |
| read_STAR | Read STAR log files |
| reexports | Objects exported from other packages |
| results2 | Extract and annotate a single DESeq results table |
| results_all | Extract and annotate all results from a DESeq analysis |
| results_apeglm | Run all results from a DESeq analysis using apeglm shrinkage |
| r_log | Regularized log transformation |
| sort_counts | Sort columns of a count matrix by rows in sample data |
| sort_samples | Sort sample names |
| summary_deseq | Summarize DESeq2 results |
| summary_tibble | Summarize tibble columns |
| top_counts | Get a count matrix of top genes |
| top_genes | Get top genes |
| write_deseq | Write DESeq results |
| write_gsea_rnk | Write DESeq results to GSEA rank file |
| write_ipa | Write DESeq results to text files for bulk uploading into IPA |
