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 27 days ago

9.47 score 44 stars 3 dependents 772 scripts 2.4k downloads

princurve - 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>.

Last updated 3 months ago

cpp

8.49 score 44 stars 26 dependents 186 scripts 3.2k 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>.

Last updated 12 hours ago

8.46 score 171 stars 76 scripts 347 downloads

SCORPIUS - Inferring Developmental Chronologies from Single-Cell RNA Sequencing Data

An accurate and easy tool for performing linear trajectory inference on single cells using single-cell RNA sequencing data. In addition, 'SCORPIUS' provides functions for discovering the most important genes with respect to the reconstructed trajectory, as well as nice visualisation tools. Cannoodt et al. (2016) <doi:10.1101/079509>.

Last updated 2 years ago

8.17 score 59 stars 126 scripts 374 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

7.53 score 74 stars 57 scripts 278 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 2 years ago

trajectory-inference

7.48 score 16 stars 1 dependents 159 scripts 573 downloads

GillespieSSA - Gillespie's Stochastic Simulation Algorithm (SSA)

Provides a simple to use, intuitive, and extensible interface to several stochastic simulation algorithms for generating simulated trajectories of finite population continuous-time model. Currently it implements Gillespie's exact stochastic simulation algorithm (Direct method) and several approximate methods (Explicit tau-leap, Binomial tau-leap, and Optimized tau-leap). The package also contains a library of template models that can be run as demo models and can easily be customized and extended. Currently the following models are included, 'Decaying-Dimerization' reaction set, linear chain system, logistic growth model, 'Lotka' predator-prey model, Rosenzweig-MacArthur predator-prey model, 'Kermack-McKendrick' SIR model, and a 'metapopulation' SIRS model. Pineda-Krch et al. (2008) <doi:10.18637/jss.v025.i12>.

Last updated 3 years ago

7.38 score 3 stars 1 dependents 96 scripts 534 downloads

dynutils - 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

cpp

6.89 score 3 stars 8 dependents 109 scripts 987 downloads

GillespieSSA2 - 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>.

Last updated 2 years ago

cpp

6.79 score 8 stars 1 dependents 51 scripts 463 downloads

laminr - Client for 'LaminDB'

Interact with 'LaminDB'. 'LaminDB' is an open-source data framework for biology. This package allows you to query and download data from 'LaminDB' instances.

Last updated 1 days ago

6.55 score 8 stars 13 scripts 372 downloads

babelwhale - 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 2 years ago

5.33 score 24 stars 2 dependents 15 scripts 742 downloads

lmds - 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 2 years ago

5.26 score 8 stars 3 dependents 10 scripts 382 downloads

qsub - Running Commands Remotely on 'Gridengine' Clusters

Run lapply() calls in parallel by submitting them to 'gridengine' clusters using the 'qsub' command.

Last updated 4 years ago

5.07 score 9 stars 37 scripts 221 downloads

diffusionMap - 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>.

Last updated 6 years ago

4.26 score 5 stars 91 scripts 424 downloads

dyndimred - 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 322 downloads

dynparam - 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 dependents 15 scripts 608 downloads

incgraph - 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.

Last updated 4 days ago

cpp

3.00 score 2 stars 3 scripts 141 downloads