Man pages for DavisLaboratory/standR
Spatial transcriptome analyses of Nanostring's DSP data in R
| addPerROIQC | Add QC statistics to the Spatial Experiment object |
| computeClusterEvalStats | Calculate statistics for evaluating batch correction |
| dkd_spe_subset | Description of the standR example datasets |
| drawPCA | Compute and plot the results of a PCA analysis on gene... |
| findBestK | Testing multiple K for RUV4 batch correction to find the best... |
| findNCGs | Get negative control genes from each batch of the data |
| geomxBatchCorrection | Batch correction for GeoMX data |
| geomxNorm | Perform normalization to GeoMX data |
| plotClusterEvalStats | Compare and evaluate different batch corrected data with... |
| plotDR | Compute and plot the results of any dimension reduction... |
| plotGeneQC | Plot gene-wise QC plot |
| plotMDS | Compute and plot the results of a MDS analysis on gene... |
| plotPairPCA | Plot pair-wise PCA plots for multiple dimensions |
| plotPCAbiplot | Plot PCA bi plot |
| plotRLExpr | Compute and plot relative log expression (RLE) values of gene... |
| plotROIQC | Plot Sample-wise QC plot |
| plotSampleInfo | Plot the user-defined meta data using alluvium plot |
| plotScreePCA | Plot the PCA scree plot. |
| prepareSpatialDecon | Preparing the inputs for SpatialDecon for doing deconvolution... |
| readGeoMx | Import GeoMX DSP data into a saptial experiment object from... |
| readGeoMxFromDGE | Import GeoMX DSP data into a spatial experiment object from... |
| spe2dge | Transfer SpatialExperiment object into DGEList object for DE... |
| standR-package | Tools for analyzing NanoString's GeoMX spatial... |
