trajectory-inference

There are 2 repositories under trajectory-inference topic.

dynverse / dynbenchmark
Comparison of methods for trajectory inference on single-cell data 🥇
trajectory-inference benchmarking bioinformatics-algorithms
Language:R 188
dynverse / dyno
Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕
trajectory trajectory-inference single-cell-omics visualisation
Language:R 161
dynverse / dynmethods
A collection of 50+ trajectory inference methods within a common interface 📥📤
single-cell-rna-seq single-cell-analysis bioinformatics-algorithms trajectory-inference-methods trajectory-inference pseudotemporal-ordering
Language:R 114
ShobiStassen / VIA
trajectory inference
trajectory-inference clustering graphs single-cell trajectory
Language:Jupyter Notebook 73
yulinliu101 / DeepTP
A deep generative model to predict aircraft actual trajectories using high dimensional weather data
trajectory-generation trajectory-prediction trajectory-inference lstm encoder-decoder encoder-decoder-model generative-model aircraft-performance gaussian-mixtures spatio-temporal deep-generative-models
Language:Jupyter Notebook 71
dynverse / dynplot
Visualising single-cell trajectories, including comparisons between two models 📈
trajectory-inference visualisation
Language:R 29
jaydu1 / VITAE
Joint Trajectory Inference for Single-cell Genomics Using Deep Learning with a Mixture Prior
tensorflow trajectory-inference python single-cell-sequencing
Language:Jupyter Notebook 25
dynverse / dynguidelines
Selecting the optimal trajectory inference based on a given dataset and user input 🔮
trajectory-inference shiny
Language:R 16
pientist / ballradar
[KDD 2023] Official implementation of "Ball Trajectory Inference from Multi-Agent Sports Contexts Using Set Transformer and Hierarchical Bi-LSTM".
machine-learning multi-agent-analysis spatiotemporal-data-analysis sports-analytics trajectory-inference
Language:Jupyter Notebook 16
dynverse / dynwrap
A common data format and inference environment for single-cell trajectories 📦
trajectory-inference
Language:R 14
StatBiomed / SingleCell-Workshop-2021
Module 4 for HKU Single-cell Workshop
single-cell-rna-seq trajectory-inference rna-velocity cellular-genetics tutorials
Language:HTML 11
xinglab-ai / genomap
Cartography of Genomic Interactions Enables Deep Analysis of Single-Cell Expression Data (Nature Communications, 2023)
bioinfomatics-pipeline bioinformatics bioinformatics-tool deep-learning genomic-data-analysis genomics genomics-visualization single-cell tabular-data biomarker-discovery biomarkers classification-algorithm data-classification multi-omic-integration regression-algorithms trajectory-inference visualization cell-annotation
Language:Python 11
aron0093 / cytopath
Simulation based inference of differentiation trajectories from RNA velocity fields.
trajectory-inference single-cell-rna-seq rna-velocity
Language:Python 10
jr-leary7 / scLANE
Characterize gene dynamics over trajectories using GLMs, GEEs, & GLMMs.
scrna-seq single-cell pseudotime trajectory-inference rna-velocity differential-expression estimating-equations genomics mixed-models transcriptomics
Language:R 7
akds / Pseudocell-Tracer
Inferring cellular trajectories from scRNA-seq using Pseudocell Tracer
pseudocell scrna-seq trajectory-inference
Language:Jupyter Notebook 5
pdmoerland / SingleCellNotes
Links to interesting courses, tutorials, papers, software etc. related to single-cell omics data analysis
single-cell trajectory-inference pseudotime-estimation spatial-transcriptomics gene-regulatory-network-inference cell-cell-interaction
5
zdong1 / CDC
Swiss CDC Project Repository: Analyze and Predict human mobility patterns using kernel density ranking methods, and analyze the spatial-temporal trends of the activity spaces of human beings.
machine-learning data-mining gps cell-phone trajectory-inference
Language:R 5
dcellwanger / CellTrails
Mirror of the Bioconductor package CellTrails (http://bioconductor.org/packages/CellTrails/)
spectral-embedding dimensionality-reduction trajectory-inference single-cell data-visualization clustering gene-expression-dynamics
Language:R 3
$fractDiffusion$ gaurav71531 / fractDiffusion
Estimate space-time fractional diffusion equation from data
fractional-diffusion trajectory-generation trajectory-inference
Language:Jupyter Notebook 3
CostaLab / phlower
Use hodge decomposition for trajectory analysis
graph-hodge-laplacain single-cell trajectory-inference
Language:Python 2
euxhenh / Truffle
Trajectory Inference of clinical data via Multi-commodity Flow
bulk-rna-seq clinical-data covid-19 crohns-disease multi-commodity-flow psoriasis time-series trajectory-inference pseudotime-ordering
Language:Jupyter Notebook 1
Nuwa
Nuwa-genomics / Nuwa
A bioinformatics web app for single cell RNA seq analysis.
bioinformatics data-science deep-learning scanpy single-cell spatial-transcriptomics streamlit trajectory-inference transcriptomics web-ui squidpy
Language:Python 1
renjun0324 / MGPfact.jl
Trajectory inference method. It can decompose complex cell trajectories into interpretable transcriptional branching Gaussian processes.
gaussian-processes single-cell trajectory-inference visualisation
Language:Julia 1
renjun0324 / MGPfactR
A model-based, unsupervised manifold learning method that factors complex cellular trajectories into interpretable bifurcating Gaussian processes of transcription.
manifold-learning single-cell trajectory-inference
Language:R 1
komparo / tde
Continuous & collaborative benchmarking of single-cell trajectory differential expression methods
trajectory-inference differential-expression
Language:R 0
MHussainy / proteo
Pseudotime analysis of OR expression during OSN differentiation
scrna-seq-analysis multigenic-monogenic-expression dynamic-expressions trajectory-inference olfactory-sensory-neurons
0
renjun0324 / ti_dbcti
A docker container for dbcti, mainly for cell trajectory inference analysis of single cell RNA-seq data
pseudotime-estimation single-cell trajectory-inference
Language:R 0
renjun0324 / ti_mgpfact
The Docker container for MGPfact is primarily used for unsupervised manifold learning of single-cell RNA-seq data and can factorize complex cell trajectories into interpretable branching Gaussian processes.
bifurcation docker gaussian-process trajectory-inference
Language:R 0
renjun0324 / ti_scfates_tree
A docker container for scFates, mainly for cell trajectory inference analysis of single cell RNA-seq data
single-cell scfates trajectory-inference
Language:Python 0

trajectory-inference

dynverse / dynbenchmark

dynverse / dyno

dynverse / dynmethods

ShobiStassen / VIA

yulinliu101 / DeepTP

dynverse / dynplot

jaydu1 / VITAE

dynverse / dynguidelines

pientist / ballradar

dynverse / dynwrap

StatBiomed / SingleCell-Workshop-2021

xinglab-ai / genomap

aron0093 / cytopath

jr-leary7 / scLANE

akds / Pseudocell-Tracer

pdmoerland / SingleCellNotes

zdong1 / CDC

dcellwanger / CellTrails

gaurav71531 / fractDiffusion

CostaLab / phlower

euxhenh / Truffle

Nuwa-genomics / Nuwa

renjun0324 / MGPfact.jl

renjun0324 / MGPfactR

komparo / tde

MHussainy / proteo

renjun0324 / ti_dbcti

renjun0324 / ti_mgpfact

renjun0324 / ti_scfates_tree

$fractDiffusion$ gaurav71531 / fractDiffusion