A guide to using a Seurat object in conjunction with RNA Velocity
Drop-in Rust + PyO3 acceleration of scvelo for single-cell RNA velocity
This repository contains single cell analysis pipelines.
Single-cell RNA velocity and cell fate trajectory inference pipeline powered by scVelo, CellRank, and AnnData. Calculates directional mRNA splicing dynamics.
Analysis of a .loom file containing single-cell RNA-sequencing data. Clustering & UMAP embedding using Scanpy, followed by RNA velocity analysis using scVelo.
RNA velocity is a high-dimensional vector that predicts the future state of individual cells on a timescale of hours.
collab | DFC
Socs3/Spp1 Project on Microglia in OIR | Ye Sun Lab Collaboration Project | Boston Children's Hospital
RNA velocity and trajectory inference (scVelo dynamical + velocity-directed PAGA + pseudotime + QC), with a fix for scv.tl.paga on current scipy. Demo on public data.
End-to-end single-cell RNA-seq analyses on public datasets — 10 reproducible projects in Scanpy & Seurat covering integration, trajectory inference, cell-cell communication, and method benchmarks.
IGFBPL1 Retinal Microglia Project | Dong Feng Chen Lab collaboration | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School
RNA velocity trajectory inference on pancreatic endocrinogenesis with a three-task benchmark evaluating trajectory recovery, rank preservation, and robustness to missing branches
Repository of the master project in Bioinformatics at Lund University
ONGOING STUDY. AFFILIATED WITH TCNHS, REGION XI, PHILIPPINES. MaligPx: A Fate Plasticity Index for Quantifying Cell-State Fate Heterogeneity in Pancreatic Ductal Adenocarcinoma. INQUIRIES: matteogalgo.ph@gmail.com
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