Software

scRNAseq processing, image processing and analysis, in silico fate mapping

Below, we provide a comprehensive list of software packages and tools that have been specifically developed for zebrahub, or that have been key for our work. These packages and tools serve a variety of purposes, including data acquisition, processing, and analysis. With these resources at their disposal, researchers can more easily and effectively work with zebrahub data, streamlining their workflows and enabling new insights and discoveries.

Sequencing

scRNAseq data

processing

repository
Gene expression variability across sibling embryos.

Gene expression

variability

repository

RNA Velocity

analysis

repository

State transition

analysis

repository

Imaging

HCR Quantification

HCR

quantification

repository

Cell Tracking

with ultrack

repository

Fate Mapping

in silico

repository

Light-sheet Data

processing

repository

Aydin

denoising

repository

Visualization

3D UMAP vizualisation

3D UMAP

visualization

repository

3D Images & Tracks

visualization

repository