anndata - 'anndata' for R (Superseded)
A 'reticulate' wrapper for the Python package 'anndata'. Provides a scalable way of keeping track of data and learned annotations. Used to read from and write to the h5ad file format. This package is superseded by 'anndataR' <https://anndataR.scverse.org>, which provides native R backends for the 'AnnData' data structure, along with conversion to/from 'SingleCellExperiment' and 'Seurat' objects.
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9.81 score 53 stars 4 dependents 1.0k scripts 3.4k downloads
dyngen - A Multi-Modal Simulator for Spearheading Single-Cell Omics Analyses
A novel, multi-modal simulation engine for studying dynamic cellular processes at single-cell resolution. 'dyngen' is more flexible than current single-cell simulation engines. It allows better method development and benchmarking, thereby stimulating development and testing of novel computational methods. Cannoodt et al. (2021) <doi:10.1038/s41467-021-24152-2>.
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benchmarkingsingle-cellsingle-cell-analysissingle-cell-omics
7.95 score 80 stars 69 scripts 578 downloads
dynwrap - Representing and Inferring Single-Cell Trajectories
Provides functionality to infer trajectories from single-cell data, represent them into a common format, and adapt them. Other biological information can also be added, such as cellular grouping, RNA velocity and annotation. Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.
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trajectory-inference
7.71 score 19 stars 167 scripts 923 downloadsdynutils - Common Functionality for the 'dynverse' Packages
Provides common functionality for the 'dynverse' packages. 'dynverse' is created to support the development, execution, and benchmarking of trajectory inference methods. For more information, check out <https://dynverse.org>.
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cpp
6.82 score 3 stars 7 dependents 106 scripts 750 downloadsbabelwhale - Talking to 'Docker' and 'Singularity' Containers
Provides a unified interface to interact with 'docker' and 'singularity' containers. You can execute a command inside a container, mount a volume or copy a file.
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5.39 score 24 stars 2 dependents 17 scripts 494 downloadslmds - Landmark Multi-Dimensional Scaling
A fast dimensionality reduction method scaleable to large numbers of samples. Landmark Multi-Dimensional Scaling (LMDS) is an extension of classical Torgerson MDS, but rather than calculating a complete distance matrix between all pairs of samples, only the distances between a set of landmarks and the samples are calculated.
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5.08 score 8 stars 2 dependents 10 scripts 307 downloadsdyndimred - Dimensionality Reduction Methods in a Common Format
Provides a common interface for applying dimensionality reduction methods, such as Principal Component Analysis ('PCA'), Independent Component Analysis ('ICA'), diffusion maps, Locally-Linear Embedding ('LLE'), t-distributed Stochastic Neighbor Embedding ('t-SNE'), and Uniform Manifold Approximation and Projection ('UMAP'). Has built-in support for sparse matrices.
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4.39 score 8 stars 31 scripts 260 downloadsdynparam - Creating Meta-Information for Parameters
Provides tools for describing parameters of algorithms in an abstract way. Description can include an id, a description, a domain (range or list of values), and a default value. 'dynparam' can also convert parameter sets to a 'ParamHelpers' format, in order to be able to use 'dynparam' in conjunction with 'mlrMBO'.
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3.80 score 3 stars 1 dependents 14 scripts 410 downloads