scater - Single-Cell Analysis Toolkit for Gene Expression Data in R
A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control and visualization.
Last updated 2 months ago
immunooncologysinglecellrnaseqqualitycontrolpreprocessingnormalizationvisualizationdimensionreductiontranscriptomicsgeneexpressionsequencingsoftwaredataimportdatarepresentationinfrastructurecoverage
6.71 score 95 dependencies 41 dependentsiheatmapr - Interactive, Complex Heatmaps
Make complex, interactive heatmaps. 'iheatmapr' includes a modular system for iteratively building up complex heatmaps, as well as the iheatmap() function for making relatively standard heatmaps.
Last updated 26 days ago
heatmapplotlyinteractive-visualizationsdata-visualizationhtmlwidgetspeer-reviewed
267 stars 6.11 score 52 dependencies 1 dependentscontrast - A Collection of Contrast Methods
One degree of freedom contrasts for 'lm', 'glm', 'gls', and 'geese' objects.
Last updated 2 years ago
2 stars 2.70 score 77 dependencies 1 dependentssnifter - R wrapper for the python openTSNE library
Provides an R wrapper for the implementation of FI-tSNE from the python package openTNSE. See Poličar et al. (2019) <doi:10.1101/731877> and the algorithm described by Linderman et al. (2018) <doi:10.1038/s41592-018-0308-4>.
Last updated 4 months ago
dimensionreductionvisualizationsoftwaresinglecellsequencing
3 stars 1.08 score 18 dependenciesBASiCStan - Stan implementation of BASiCS
Provides an interface to infer the parameters of BASiCS using the variational inference (ADVI), Markov chain Monte Carlo (NUTS), and maximum a posteriori (BFGS) inference engines in the Stan programming language. BASiCS is a Bayesian hierarchical model that uses an adaptive Metropolis within Gibbs sampling scheme. Alternative inference methods provided by Stan may be preferable in some situations, for example for particularly large data or posterior distributions with difficult geometries.
Last updated 4 months ago
immunooncologynormalizationsequencingrnaseqsoftwaregeneexpressiontranscriptomicssinglecelldifferentialexpressionbayesiancellbiology
0.71 score 153 dependencies