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

Testing it out | Testing and continuous integration | Creating an example dataset | Continuous integration

Definition | Run function | Testing it out | Making your method available for other users

definition.yml | Interactive development | Making your method available for other users | Wrapping a method without dyncli(py)

Set up | Download and load dataset | Preprocessing dataset | Analysing your dataset in R

Creating an AnnData object | Reading / writing AnnData objects | Creating a view | AnnData as a matrix | Note on state

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

System requirements | Step 1: Installing from CRAN or GitHub (Required) | Step 2: Configure host system (Recommended) | Step 3: Download cacheable files (Optional)

Step 1: Define backbone and other parameters | Step 2: Generate transcription factors (TFs) | Step 3: Sample target genes and housekeeping genes (HKs) | Step 4: Generate kinetics | Step 5: Simulate gold standard | Step 6: Simulate cells. | Step 7: Experiment emulation | Step 8: Convert to a dyno object | Step 8 alternative: Convert to an anndata/SCE/Seurat object | One-shot function

Common trajectory model | Direct wrapping | Indirect wrapping