anndataR - AnnData interoperability in R
Bring the power and flexibility of AnnData to the R ecosystem, allowing you to effortlessly manipulate and analyse your single-cell data. This package lets you work with backed h5ad and zarr files, directly access various slots (e.g. X, obs, var), or convert the data into SingleCellExperiment and Seurat objects.
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singlecelldataimportdatarepresentationanndatah5adinteroperability
12.10 score 196 stars 4 dependents 319 scripts 2.0k downloadsanndata - 'anndata' for R (Superseded)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 This package is superseded by 'anndataR' 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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9.47 score 53 stars 4 dependents 1.3k scripts 2.4k downloadsprincurve - Fit a Principal Curve in Arbitrary Dimension
Fitting a principal curve to a data matrix in arbitrary dimensions. Hastie and Stuetzle (1989) <doi:10.2307/2289936>.
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cpp
9.43 score 45 stars 28 dependents 251 scripts 19k 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
8.09 score 83 stars 92 scripts 661 downloads
funkyheatmap - Generating Funky Heatmaps for Data Frames
Allows generating heatmap-like visualisations for data frames. Funky heatmaps can be fine-tuned by providing annotations of the columns and rows, which allows assigning multiple palettes or geometries or grouping rows and columns together in categories. Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.
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7.98 score 202 stars 119 scripts 614 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
7.78 score 19 stars 199 scripts 715 downloadsGillespieSSA2 - Gillespie's Stochastic Simulation Algorithm for Impatient People
A fast, scalable, and versatile framework for simulating large systems with Gillespie's Stochastic Simulation Algorithm ('SSA'). This package is the spiritual successor to the 'GillespieSSA' package originally written by Mario Pineda-Krch. Benefits of this package include major speed improvements (>100x), easier to understand documentation, and many unit tests that try to ensure the package works as intended. Cannoodt and Saelens et al. (2021) <doi:10.1038/s41467-021-24152-2>.
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cpp
7.12 score 9 stars 1 dependents 98 scripts 565 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
6.86 score 3 stars 7 dependents 115 scripts 983 downloadsqsub - Running Commands Remotely on 'Gridengine' Clusters
Run lapply() calls in parallel by submitting them to 'gridengine' clusters using the 'qsub' command.
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5.12 score 9 stars 42 scripts 299 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 560 downloadsdiffusionMap - Diffusion Map
Implements diffusion map method of data parametrization, including creation and visualization of diffusion map, clustering with diffusion K-means and regression using adaptive regression model. Richards (2009) <doi:10.1088/0004-637X/691/1/32>.
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4.50 score 6 stars 83 scripts 1.6k 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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4.50 score 24 stars 1 dependents 22 scripts 643 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 446 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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3.92 score 4 stars 1 dependents 14 scripts 607 downloadsincgraph - Incremental Graphlet Counting for Network Optimisation
An efficient and incremental approach for calculating the differences in orbit counts when performing single edge modifications in a network. Calculating the differences in orbit counts is much more efficient than recalculating all orbit counts from scratch for each time point.
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cpp
3.00 score 2 stars 6 scripts 288 downloads