Man pages for stela2502/BioData
The package allows to annotate a numeric data.table with col and row data
| addCellCyclePhase-methods | description of function addCellCyclePhase |
| add_to_stat-methods | Add a stsitics table to the $stats slot |
| as_BioData | create a BioData from an other object |
| as_BioData-methods | description of function as_BioData |
| as_cellexalvr | description of function as_cellexalvr |
| as_cellexalvr-methods | description of function as_cellexalvr |
| as_Seurat-methods | convert BioData to Seurat |
| auto_order_grouping-methods | Auto re-order a (RF) grouping |
| auto_reorder_grouping-methods | automaticly reorder a grouping based on summmary expression... |
| bestGrouping | description of function randomForest |
| CellCycle | A simple table containing the Human and mouse orthologe... |
| CellCycleGenes | A simple table containing the Human and mouse orthologe... |
| changeNames-methods | description of function changeNames |
| cleanUpGroup-methods | description of function cleanUpGroup |
| clusters_gene-methods | description of function clusters_gene |
| clusters-methods | create a grouping based on either the raw data or a MDS... |
| CodonHeatmap-methods | description of function heatmap |
| collapse2codons-methods | description of function collapse2codons |
| collapse-methods | description of function collapse |
| collaps-methods | description of function collaps |
| colnames-methods | warpper for colnames(x$dat) |
| colors_4-methods | description of function createRFgrouping_col |
| combineGroupings-methods | description of function combineGroupings |
| complexHeatmap-methods | description of function complexHeatmap |
| convert_to-methods | description of function convert_to |
| copy_grouping-methods | Copy a grouping (samples column) from one to another BioData... |
| copy_mds_objects-methods | copy MDS structures and checking that the dimensions and... |
| Cpp_FindAllMarkers-methods | description of function Cpp_FindAllMarkers |
| CreateBin-methods | Create a binned annotation column from numeric data |
| createDuplicates-methods | description of function createDuplicates |
| createRFgrouping_col-methods | description of function createRFgrouping_col |
| createRFgrouping_row-methods | description of function createRFgrouping_row |
| createStats-methods | description of function createStats |
| dataframe2biodata-methods | description of function dataframe2biodata |
| defineGOIs-methods | description of function defineGOIs |
| define_grouping-methods | description of function define_grouping |
| defineHeatmapColors-methods | description of function defineHeatmapColors |
| DimReduction | initial dimensional reduction step based on PCA |
| Epigenetic | A simple table containing the data from... |
| export.data-methods | description of function write.data |
| extractCodonInformation-methods | description of function extractCodonInformation |
| filterGenes-methods | description of function filterGenes |
| findDuplicates-methods | description of function findDuplicates |
| findOverlapWithCells-methods | description of function findOverlapWithCells |
| fit_4_rf-methods | Reduce memory footprint and -1 values from a BioData object |
| force.numeric-methods | description of function force.numeric |
| getEnsembl-methods | description of function getEnsembl |
| getGeneInfo-methods | description of function getEnsembl |
| get.genes.cor.to-methods | description of function get.genes.cor.to |
| getGenesExpressedHigherThanExpected-methods | description of function getGenesExpressedHigherThanExpected |
| getNgenesFromMultiGroupStats-methods | description of function getNgenesFromMultiGroupStats |
| Get_PartialTest_Obj-methods | description of function Get_PartialTest_Obj |
| getSymbols-methods | description of function getSymbols |
| getTopSigGenes-methods | obtain a list of most significant genes per comparison froma... |
| group_intersect_order-methods | description of function group_intersect_order |
| groups_boxplot-methods | description of function groups_boxplot |
| H5Anno2df-methods | description of function H5Anno2df |
| heatPlotTimelines2D-methods | description of function heatPlotTimelines2D |
| human.CellSurface | A simple list containing the human ENTREZ.gene.symbols from... |
| human.tfs | A list of human transcription factors. |
| IdentifyMarkerGenes-methods | description of function IdentifyMarkerGenes |
| load_CellexalVR_selection-methods | description of function load_CellexalVR_selection |
| loadObj-methods | description of function loadObj |
| logThis-methods | description of function log |
| Make3D4obj-methods | description of function Make3D4obj |
| mds-methods | Calculate MDS projections for the 3D Make3Dobj function |
| merge_cells-methods | description of function merge_cells |
| merge-methods | merge 2 or more BioData objects |
| MicroArray | Class interface for two coor microarray data |
| mouse.CellSurface | A simple list containing the mouse ENTREZ.gene.symbols from... |
| mouse.tfs | A list of mouse transcription factors. |
| normalize | normalize a BioData::R6 object |
| normalize_R_buggy | normalize a SingleCells::BioData::R6 object |
| ontologyLogPage-methods | description of function ontologyLogPage |
| PartialTests-methods | description of function PartialTests |
| plot2col_barplot-methods | description of function plot2col_barplot |
| plotCodonUsage-methods | description of function plotCodonUsage |
| plotLegend-methods | description of function plot.legend |
| plotMDS-methods | description of function plotMDS |
| plot_velocyto-methods | description of function plot_velocyto |
| positivesOnly-methods | description of function positivesOnly |
| preprocess-methods | description of function preprocess |
| pseudotimeTest3D-methods | description of function pseudotimeTest3D |
| pseudotimeTest-methods | description of function pseudotimeTest |
| pwd-methods | description of function pwd |
| quality_of_fit-methods | description of function quality_of_fit |
| readLoomFile-methods | description of function readLoomFile |
| reduceTo-methods | description of function reduceTo |
| removeNeg-methods | description of function removeNeg |
| renew-methods | description of function renew |
| reorder.genes-methods | Class a simple interface to biological data (numeric) and... |
| reorder_grouping-methods | description of function reorder_grouping |
| reorder_on_wilcox_results-methods | description of function reorder_on_wilcox_results |
| reorder.samples-methods | description of function remove.genes |
| rfCluster_col | rfCluster_col |
| rfCluster_row | rfCluster_row |
| rmdLink-methods | easily create an Rmd link that opens in a new window. |
| rownames-methods | wrapper for rownames(x$dat) |
| runStats_inThread-methods | description of function runStats_inThread |
| sampleCodonUsage-methods | description of function sampleCodonUsage |
| saveObj-methods | description of function saveObj |
| Seurat_FindAllMarkers-methods | description of function Seurat_FindAllMarkers |
| SeuratVarGenes-methods | description of function SeuratVarGenes |
| show-methods | description of function show |
| simpleAnova-methods | description of function simpleAnova |
| SingleCells | Class interface for single cell data |
| Split4Geo-methods | description of function Split4Geo |
| SQLite_ExpressionSummary-methods | description of function SQLite_ExpressionSummary |
| SQLite_SampleSummary-methods | description of function SQLite_SampleSummary |
| stat_table-methods | description of function stat_table |
| TestData | merged the two smallest Mouse Tabular muris datasets... |
| transpose-methods | description of function t |
| tRF.typeHeatmap-methods | description of function heatmap |
| tRNAMINT | Class interface for the MINT output |
| tRNA_stats-methods | description of function tRNA_stats |
| useInbuiltGOIlists-methods | description of function useInbuiltGOIlists |
| vioplot-methods | description of function vioplot |
| z.score-methods | description of function z.score |
