anndata - 'anndata' for R
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.
Last updated 7 days ago
9.16 score 43 stars 3 packages 604 scripts 2.1k 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>.
Last updated 2 years ago
benchmarkingsingle-cellsingle-cell-analysissingle-cell-omics
7.50 score 73 stars 54 scripts 314 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>.
Last updated 1 years ago
trajectory-inference
7.46 score 15 stars 1 packages 161 scripts 552 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>.
Last updated 2 years ago
6.86 score 3 stars 8 packages 101 scripts 845 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.
Last updated 1 years ago
5.33 score 24 stars 2 packages 15 scripts 624 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.
Last updated 1 years ago
5.26 score 8 stars 3 packages 10 scripts 432 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.
Last updated 4 years ago
4.21 score 7 stars 23 scripts 332 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'.
Last updated 6 years ago
3.95 score 2 stars 2 packages 15 scripts 462 downloads