Welcome to TIVelo's documentation! ================================== .. figure:: ../fig/workflow_1.png :align: center Workflow of TIVelo RNA velocity inference is a valuable tool for understanding cell development, differentiation, and disease progression. However, existing RNA velocity inference methods typically rely on explicit assumptions of ordinary differential equations (ODE), which prohibits them to capture complex transcriptome expression patterns. In this study, we introduce TIVelo, a novel RNA velocity estimation approach that first determines the velocity direction at the cell cluster level based on trajectory inference, before estimating velocity for individual cells. TIVelo calculates an orientation score to infer the direction at the cluster level without an explicit ODE assumption, which effectively captures complex transcriptional patterns, avoiding potential inconsistencies in velocity estimation for genes that do not follow the simple ODE assumption. We validated the effectiveness of TIVelo by its application to 16 real datasets and the comparison with five benchmarking methods. .. note:: This project is under active development. User Guide ---------- To run baseline, we need to install:: pip install --upgrade pip pip install tensorflow==2.10.0 pip install unitvelo==0.2.5.2 multivelo==0.1.3 velovi==0.3.1 .. toctree:: :maxdepth: 2 install tivelo Tutorials ---------------- Commonly-used RNA velocity datasets ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. toctree:: :maxdepth: 1 notebooks/notebooks/Pancreas notebooks/notebooks/DentateGyrus notebooks/notebooks/DentateGyrus2 notebooks/notebooks/Erythroid notebooks/notebooks/Hindbrain notebooks/notebooks/Reprogramming notebooks/notebooks/Organoid notebooks/notebooks/Retina notebooks/notebooks/scNT notebooks/notebooks/Hindbrain2 Datasets with scATAC-seq ~~~~~~~~~~~~~~~~~~~~~~~~ .. toctree:: :maxdepth: 1 notebooks/notebooks/HSPCs notebooks/notebooks/HumanBrain notebooks/notebooks/MouseBrain notebooks/notebooks/MouseSkin FUCCI datasets ~~~~~~~~~~~~~~ .. toctree:: :maxdepth: 1 notebooks/notebooks/U2OS notebooks/notebooks/RPE1