Man pages for ImmuneDynamics/Spectre
High-dimensional cytometry and imaging analysis
| adjust.files | adjust.files |
| check.files | check.files |
| create.dt | create.dt - convert a Seurat or SingleCellExperiment to a... |
| create.stats | create.stats - perform statistical analysis and generate an... |
| create.sumtable | create.sumtable - create a data.table 'summarising' cellular... |
| demo.clustered | demo.clustered - Demo data.table with cells (rows) x markers... |
| do.add.cols | do.add.cols |
| do.add.masks | do.add.masks |
| do.add.percell | do.add.percell |
| do.aggregate | Aggregate data using data.table functions - summarises the... |
| do.align | do.align - Function to align multiple batches of a dataset. |
| do.asinh | do.asinh - Transform data in selected columns using ArcSinH |
| do.calculate.area | do.calculate.area |
| do.clip | do.clip - Clips data using a specified lower and upper value |
| do.combine.cols | do.combine.cols - Combine the values of two columns into a... |
| do.create.outlines | do.create.outlines |
| do.extract | do.extract |
| do.extract.cell.dat | do.extract.cell.dat |
| do.filter | do.filter - filtering data.table using multiple match values |
| do.filter.percell | do.filter.percell |
| do.label.from.polygon | do.label.from.polygon |
| do.list.summary | Summarise the column names and row numbers for elements of a... |
| do.list.switch | List switch or inversion |
| do.logicle | Using logicle to transform data |
| do.merge.files | do.merge.files - Function to merge a list of data.tables (one... |
| do.pull.data | do.pull.data |
| do.reorder | do.reorder - custom row re-ordering of a data.table |
| do.rescale | do.rescale - Re-scale data in selected columns between two... |
| do.stats | Statistical analysis |
| do.subsample | Subsample data |
| do.zscore | do.zscore - Calculate z.score for a dataset |
| fast.colour.plot | Create a FAST dot plot (X vs Y) coloured by a selected... |
| fast.multi.plot | Make FAST multiple plots for multiple columns and/or multiple... |
| fftRtsne | FIt-SNE Based on Kluger Lab FIt-SNE |
| make.autograph | make.autograph - Creates plots using ggplot2 |
| make.colour.plot | Create a dot plot (X vs Y) coloured by a selected continuous... |
| make.multi.plot | Make multiple plots for multiple columns and/or multiple... |
| make.pheatmap | make.pheatmap - Create a 'pretty' heatmap (pheatmap) |
| make.spatial.plot | make.spatial.plot |
| make.volcano.plot | Make an enhanced volcano plot |
| package.check | package.check - a function to check the installation of all... |
| package.install | package.install - a function to install packages required for... |
| package.load | package.load - a function to load (library) all required... |
| prep.cytonorm | prep.cytonorm - Prepare reference data into a FlowSOM object |
| read.files | read.files - Function to read data from CSV or FCS files into... |
| read.spatial.files | Read TIFF files into R and and create spatial data object |
| run.align | run.align - Run the alignment model on a target data.table |
| run.cytonorm | run.cytonorm - Run the alignment model on a target data.table |
| run.fitsne | Run FIt-SNE, Fourier Transform TSNE. |
| run.flowsom | Run the FlowSOM algorithm |
| run.harmony | run.harmony - dun Harmony alignment on a data.table |
| run.knn.classifier | run.knn.classifier - Run KNN classifier |
| run.pca | Run the PCA algorithm (using stats::prcomp) |
| run.phenograph | run.phenograph - Run phenograph clustering |
| run.rpca | Run rPCA for batch correction |
| run.ruv | run.ruv - Run the the CytofRUV alignment method. |
| run.spatial.analysis | run.spatial.analysis |
| run.tsne | Run the tSNE algorithm (using Rtsne::Rtsne()) |
| run.umap | Run the UMAP algorithm (using umap::umap()) |
| spatial-class | spatial object |
| train.cytonorm | train.cytonorm - Prepare reference data into a FlowSOM object |
| train.knn.classifier | train.knn.classifier - Train KNN classifier |
| write.files | write.files - Write .csv or .fcs files |
| write.hdf5 | write.hdf5 |
