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sbfnk

rbi:Interface to 'LibBi'

Provides a complete interface to 'LibBi', a library for Bayesian inference (see <https://libbi.org> and Murray, 2015 <doi:10.18637/jss.v067.i10> for more information). This includes functions for manipulating 'LibBi' models, for reading and writing 'LibBi' input/output files, for converting 'LibBi' output to provide traces for use with the coda package, and for running 'LibBi' to conduct inference.

Maintained by Sebastian Funk. Last updated 10 months ago.

24 stars 8.35 score 390 scripts 1 dependents

rcannood

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>.

Maintained by Robrecht Cannoodt. Last updated 2 years ago.

59 stars 8.17 score 126 scripts

dynverse

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>.

Maintained by Robrecht Cannoodt. Last updated 2 years ago.

benchmarkingsingle-cellsingle-cell-analysissingle-cell-omics

74 stars 7.53 score 57 scripts

bioc

BERT:High Performance Data Integration for Large-Scale Analyses of Incomplete Omic Profiles Using Batch-Effect Reduction Trees (BERT)

Provides efficient batch-effect adjustment of data with missing values. BERT orders all batch effect correction to a tree of pairwise computations. BERT allows parallelization over sub-trees.

Maintained by Yannis Schumann. Last updated 2 months ago.

batcheffectpreprocessingexperimentaldesignqualitycontrolbatch-effectbioconductor-packagebioinformaticsdata-integrationdata-science

2 stars 5.40 score 18 scripts

cran

simuclustfactor:Simultaneous Clustering and Factorial Decomposition of Three-Way Datasets

Implements two iterative techniques called T3Clus and 3Fkmeans, aimed at simultaneously clustering objects and a factorial dimensionality reduction of variables and occasions on three-mode datasets developed by Vichi et al. (2007) <doi:10.1007/s00357-007-0006-x>. Also, we provide a convex combination of these two simultaneous procedures called CT3Clus and based on a hyperparameter alpha (alpha in [0,1], with 3FKMeans for alpha=0 and T3Clus for alpha= 1) also developed by Vichi et al. (2007) <doi:10.1007/s00357-007-0006-x>. Furthermore, we implemented the traditional tandem procedures of T3Clus (TWCFTA) and 3FKMeans (TWFCTA) for sequential clustering-factorial decomposition (TWCFTA), and vice-versa (TWFCTA) proposed by P. Arabie and L. Hubert (1996) <doi:10.1007/978-3-642-79999-0_1>.

Maintained by Prosper Ablordeppey. Last updated 2 years ago.

1.70 score

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