rna-velocity

There are 1 repository under rna-velocity topic.

aristoteleo / dynamo-release
Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses
dynamo scslam-seq scrna-seq vector-field potential-landscape nasc-seq sci-fate scnt-seq rna-velocity cell-fate dynamical-systems differential-geometry rna-jacobian rna-acceleration rna-curvature rna-divergence
Language:Python 401
cellrank
theislab / cellrank
CellRank: dynamics from multi-view single-cell data
machine-learning single-cell-rna-seq bioinformatics rna-velocity markov-chains genetics data-science fuzzy-clustering-analyses manifold-learning single-cell-genomics trajectory-generation cell-fate-transitions cell-fate-determination
Language:Python 298
basilkhuder / Seurat-to-RNA-Velocity
A guide to using a Seurat object in conjunction with RNA Velocity
seurat integrating-loom kallisto bustools kb-python rna-velocity anndata velocyto scvelo kallisto-bustools
122
GuangyuWangLab2021 / cellDancer
Predict RNA velocity through deep learning
cell-fate rna-splicing rna-splicing-analysis rna-velocity rna-velocity-estimation single-cell-genomics single-cell-rna-seq transcriptomics
Language:Jupyter Notebook 51
kevinrue / velociraptor
Toolkit for Single-Cell Velocity
rna-velocity
Language:R 51
pyrovelocity
pinellolab / pyrovelocity
𝒫robabilistic modeling of RNA velocity ⬱
cell-fate-determination deep-generative-model developmental-trajectories multiomics probabilistic-models probabilistic-programming rna-velocity rna-velocity-estimation single-cell-genomics single-cell-rna-seq transcriptomics rna-splicing rna-splicing-analysis single-cell-multiomics pyro
Language:Python 34
calico / velodyn
Dynamical systems methods for RNA velocity analysis
single-cell rna-seq rna-velocity dynamical-systems
Language:Python 23
aristoteleo / dynast-release
Inclusive and efficient quantification of labeling and splicing RNAs for time-resolved metabolic labeling based scRNA-seq experiments
metabolic-labeling scrna-seq rna-velocity vector-field scnt-seq scslam-seq sci-fate nasc-seq
Language:Python 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
aron0093 / cytopath
Simulation based inference of differentiation trajectories from RNA velocity fields.
rna-velocity single-cell-rna-seq trajectory-inference
Language:Python 10
TheJacksonLaboratory / STQ
Spatial Transcriptomics Quantification pipeline for 10x Visium and H&E-stained whole slide images
he-stained-wsi rna-velocity spatial-transcriptomics species-deconvolution visium xengsort xenome
Language:Python 9
huangyh09 / brie-tutorials
Tutorials for using BRIE
single-cell-rna-seq alternative-splicing rna-velocity differential-splicing differential-momentum-genes variational-inference
Language:Jupyter Notebook 7
jr-leary7 / scLANE
Characterize gene dynamics over trajectories using GLMs, GEEs, & GLMMs.
differential-expression estimating-equations genomics mixed-models pseudotime rna-velocity scrna-seq single-cell trajectory-inference transcriptomics
Language:R 7
theimagelab / entrain
Entrain: Predicting Environmental Regulators of Differentiation Trajectories
cell-cell-communication cell-fate differentiation microenvironment rna-velocity single-cell trajectory-analysis
Language:R 6
sqjin / nlvelo
R pacakge for RNA velocity estimation with nonlinear models
cellulardynamics rna-velocity single-cell
Language:R 4
hisplan / docker-velocyto
Dockerized Velocyto for RNA Velocity
rna-velocity docker
Language:Dockerfile 2
RGC_Dnmt3a_pONC2d_paper
mcrewcow / RGC_Dnmt3a_pONC2d_paper
Retinal ganglion cells regeneration in 2 days post optic nerve crush retina | Lydia Tai | Dong Feng Chen Lab collaboration | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School
bioinformatics cellchat epigenetics gsea pathway-analysis python r regeneration retinal-ganglion-cell rna rna-velocity sequencing seurat single-cell single-cell-rna-sequencing single-nuclei single-nuclei-rna-sequencing transcriptome velocity optic-nerve-crush
Language:R 1
mcrewcow / ChaginLab
Growth Hormone effect on Cartilage Growth Plate; Light-Sheet Microscopy; Pseudocoloring | Projects I started and still working on in Andrei Chagin Lab | Karolinska Institutet
bone cartilage cellchat light-sheet-microcopy pseudocolor python r rna rna-velocity seurat single-cell stem-cells velocity
Language:Jupyter Notebook 0
mcrewcow / Pan_et_al_DFChen_IGFPL1_paper
IGFBPL1 Retinal Microglia Project | Dong Feng Chen Lab collaboration | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School
bioinformatics forceatlas2 glaucoma microglia ophtalmology rna-seq rna-seq-analysis rna-velocity scanpy scvelo single-cell transcriptomics velocyto
Language:Jupyter Notebook 0
mcrewcow / Sun_Ye_microglia_macrophages_paper
Socs3/Spp1 Project on Microglia in OIR | Ye Sun Lab Collaboration Project | Boston Children's Hospital
cellchat forceatlas2 macrophage microglia python r rna rna-velocity scanpy scvelo seurat single-cell transcriptomics velocity gobp oir socs3 spp1
Language:Jupyter Notebook 0
hisplan / velopipe
RNA Velocity for SEQC
rna-velocity wdl seqc
Language:WDL
mayurdoke6 / Longitudinal-scRNAseq-of-human-pancreatic-slices
This repository contains coding scripts utilized for the analysis of Longitudinal scRNAseq of human pancreatic slices datasets
longitudinal-data rna-velocity scrna-seq-analysis
Language:R
mcrewcow / Yizhen_microglia
collab | DFC
bash forceatlas2 python r rna-seq rna-velocity scanpy scvelo seurat single-cell single-cell-rna-seq splicing transcriptomics ubuntu
Language:Jupyter Notebook