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Read/write Seurat objects using anndataR2 months ago
Introduction | Prerequisites | Reading H5AD files and Zarr stores to a Seurat Object | Mapping between AnnData and Seurat | Writing a Seurat object to a H5AD file or Zarr store | Session info
Read/write SingleCellExperiment objects using anndataR2 months ago
Introduction | Prerequisites | Reading H5AD files and Zarr stores to a SingleCellExperiment object | Mapping between AnnData and SingleCellExperiment | Writing a SingleCellExperiment object to a H5AD file or Zarr store | Session info
Using anndataR2 months ago
Introduction | Relationship to other packages | Installation | Usage | Read from disk | Using AnnData objects | Interoperability | Manually create an AnnData object | Write to disk | Subsetting AnnData objects | Basic subsetting | Combined subsetting | Using different index types | Working with views | Citing anndataR | Session info
Migrating from anndata to anndataR2 months ago
Why migrate? | Installation | Side-by-side migration guide | Creating an AnnData object | Reading and writing h5ad files | Slot access and subsetting | Interoperability (new in anndataR) | Using ReticulateAnnData as a stepping stone | Getting help with anndataR
Creating a TI method: Container2 months ago
Testing it out | Testing and continuous integration | Creating an example dataset | Continuous integration
Creating a TI method: R2 months ago
Definition | Run function | Testing it out | Making your method available for other users
Creating a TI method: Script2 months ago
definition.yml | Interactive development | Making your method available for other users | Wrapping a method without dyncli(py)
Python Integration with anndataR3 months ago
Introduction | Prerequisites | Basic Integration with scanpy | Conversion to R objects | Multi-modal data with mudata | Session info | R | Python
Demo with scanpy1 years ago
Set up | Download and load dataset | Preprocessing dataset | Analysing your dataset in R
Getting started1 years ago
Creating an AnnData object | Reading / writing AnnData objects | Creating a view | AnnData as a matrix | Note on state
Getting started with funkyheatmap1 years ago
Loading the data | Adding column_info | Adding palettes | Adding column_groups | Specifying geoms | Customising legends | Adding images | Row grouping
Recreating the scIB figures2 years ago
Introduction | Summary figure | Data | Column information | Row information | Palettes | Legends | Figure | References
Decaying-Dimerization Reaction Set3 years ago
References
Kermack-McKendrick SIR model3 years ago
References
Linear Chain System3 years ago
References
Lotka Predator-Prey model3 years ago
Pearl-Verhulst Logistic Growth model3 years ago
References
Radioactive Decay model3 years ago
References
Rosenzweig-MacArthur Predator-Prey model3 years ago
References
SIRS metapopulation model3 years ago
References
Overview of the functionality provided by the dynutils package4 years ago
Table of contents | Manipulation of lists | add_class: Add a class to an object | extend_with: Extend list with more data | Calculations | calculate_distance: Compute pairwise distances between two matrices | project_to_segments: Project a set of points to to set of segments | calculate_mean: Calculate a (weighted) mean between vectors or a list of vectors; supports the arithmetic, geometric and harmonic mean | Manipulation of matrices | expand_matrix: Add rows and columns to a matrix | Scaling of matrices and vectors | scale_uniform: Rescale data to have a certain center and max range | scale_minmax: Rescale data to a [0, 1] range | scale_quantile: Cut off outer quantiles and rescale to a [0, 1] range | Manipulation of functions | inherit_default_params: Have one function inherit the default parameters from other functions | Manipulation of packages | check_packages: Easily checking whether certain packages are installed | install_packages: Install packages taking into account the remotes of another | Manipulation of vectors | random_time_string: Generates a string very likely to be unique | Tibble helpers | list_as_tibble: Convert a list of lists to a tibble whilst retaining class information | tibble_as_list: Convert a tibble back to a list of lists whilst retaining class information | extract_row_to_list: Extracts one row from a tibble and converts it to a list | mapdf: Apply a function to each row of a data frame | File helpers | safe_tempdir: Create an empty temporary directory and return its path | Assertion helpers | %all_in%: Check whether a vector are all elements of another vector | %has_names%: Check whether an object has certain names | is_single_numeric: Check whether a value is a single numeric | is_bounded: Check whether a value within a certain interval
Installation instructions5 years ago
Getting started6 years ago
Converting from GillespieSSA to GillespieSSA26 years ago
Introduction to GillespieSSA26 years ago
Creating a TI method: Wrapping trajectories7 years ago
Common trajectory model | Direct wrapping | Indirect wrapping
Decaying-Dimerization Reaction Set (Gillespie, 2001)7 years ago
Kermack-McKendrick SIR model (Brown & Rothery, 1993)7 years ago
Linear Chain System (Cao et al., 2004)7 years ago
Lotka predator-prey model (Gillespie, 1977; Kot, 2001)7 years ago
Pearl-Verhulst Logistic growth model (Kot, 2001)7 years ago
Radioactive decay model (Gillespie, 1977)7 years ago
Rosenzweig-MacArthur predator-prey model (Pineda-Krch et al., 2007)7 years ago
SIRS metapopulation model (Pineda-Krch, 2008)7 years ago