dynverse: benchmarking, constructing and interpreting single-cell trajectories
The dynverse is an open set of packages to benchmark, construct and interpret single-cell trajectories. See https://dynverse.org for an overview
The dynverse
Pinned Repositories
anndata
Annotated multivariate observation data in R
babelwhale
Talking to Docker and Singularity containers
dynbenchmark
Comparison of methods for trajectory inference on single-cell data 🥇
dyngen
Simulating single-cell data using gene regulatory networks 📠
dynguidelines
Selecting the optimal trajectory inference based on a given dataset and user input 🔮
dynmethods
A collection of 50+ trajectory inference methods within a common interface 📥📤
dyno
Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕
dynplot
Visualising single-cell trajectories, including comparisons between two models 📈
dynverse
A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍
lmds
Landmark Multi-Dimensional Scaling
dynverse: benchmarking, constructing and interpreting single-cell trajectories's Repositories
dynverse/competition
Topcoder single-cell trajectory inference competition
dynverse/dyneval
Metrics to compare two or more trajectories ⚖
dynverse/travis_scripts
Helper scripts for testing containers on Travis
dynverse/emojifont
:lollipop:Emoji and fontawesom in both base and ggplot2 graphics
dynverse/funky_cover
dynverse/netdist
Network distances
dynverse/dynclipy
Tiny wrapper for python around dynwrap/dyncli for python
dynverse/dynmethods_automated_testing
Automated testing results of dynmethods at https://dynverse.github.io/dynmethods_automated_testing/index.html
dynverse/dynvelocity
combining trajectories and RNA velocity
dynverse/dynwrap_tester
Small example TI method within a docker
dynverse/ElPiGraph.R
An R package to construct Elastic Principal Graphs
dynverse/embeddr
Pseudotemporal ordering of single-cell RNA-seq data using laplacian eigenmaps & principal curves
dynverse/hexbin
community curated list of hexagon logos
dynverse/merlot
Reconstruct the lineage topology of a scRNA-seq differentiation daatset.
dynverse/Mpath
Unofficial R package for the Mpath trajectory inference method
dynverse/pCreode
An algorithm for mapping cell state transitions.
dynverse/preproc
dynverse/pseudogp
Probabilistic pseudotime for single-cell RNA-seq data
dynverse/PySCUBA
Python for Single-cell Clustering Using Bifurcation Analysis
dynverse/pywishbone
Wishbone is an algorithm to align cells along developmental trajectories with branches
dynverse/reCAT
dynverse/scaterlegacy
Legacy version of scater
dynverse/SCIMITAR
Single Cell Inference of MorphIng Trajectories and their Associated Regulation (SCIMITAR)
dynverse/SLICE
A method for calculating single cell entropy and reconstructing cell differentiation lineage using single-cell RNA-seq data
dynverse/spark
dynverse/topslam_R
dynverse/tradeSeq
TRAjectory-based Differential Expression analysis for SEQuencing data
dynverse/travis_hdf5
Builds for hdf5 on travis
dynverse/URD
URD - Reconstruction of Branching Developmental Trajectories
dynverse/Wishbone