pseudotime-trajectory

Aligning gene expression trajectories of single-cell reference and query systems

MiCV is a python dash-based web-application that enables researchers to upload raw scRNA-seq data and perform filtering, analysis, and manual annotation.

An R package providing tools for single-cell RNA-seq data analysis, enhancing existing methods with helper functions.

Trajectory-guided dimension reduction for multi-sample single-cell RNA-seq data

Computationally efficient modeling of temporal and spatial gene expression patterns

Trajectory analysis on scRNA-seq data from SARS-CoV-2-infected human bronchial epithelial cells (HBEC). Scanpy. Dataset Source: Ravindra et al. (2021). Single-cell longitudinal analysis of SARS-CoV-2 infection in human airway epithelium identifies target cells, alterations in gene expression, and cell state changes. PLoS Biology, 19(3), e3001143.

scRNA-seq of ADAR1-KO melanoma TME — pDC/monocyte ISG programs, PAGA pseudotime, TCGA SKCM survival validation | Scanpy · Python

Transcription-Factor Aided RNA Velocity Inference: a deep generative (VAE) extension of VeloVI with cell-specific TF-regulated transcription rates (ChEA/ENCODE), a supervised residual latent-time head, a velocity-time consistency loss, and velocity-pseudotime blending for calibrated cell-fate trajectories from scRNA-seq.