{"repo":"jfnavarro/st_viewer","free":true,"listed":false,"github":"https://github.com/jfnavarro/st_viewer","clone":"git clone https://github.com/jfnavarro/st_viewer.git","description":"A GUI tool for easy and smooth visualisation and analysis of Spatial Transcriptomics datasets","language":"C++","stars":11,"topics":["viewer","spatial-analysis","spatial-transcriptomics","machine-learning","data-analysis","data-visualization","3d","opengl"],"license":null,"category":"machine-learning","readme_excerpt":"Spatial Transcriptomics Viewer The ST viewer is a tool that can be used to visualize and analize spatially resolved gene expression data in 3D (consecutive sections) or in 2D (with the HE stained tissue image). The ST Viewer is cross platform which means that it can be built and run in OSX, LINUX and WINDOWS. The ST viewer allows interaction with the data in real time. Users can see where specific genes are expressed and how expressed they are. It has different threshold, normalization and visualization options. It also allows to select areas of the tissue to obtain gene patterns to later do DEA or spot classification using machine learning. The ST viewer requires as input a matrix of counts in TSV format where genes are columns and spot ids are rows. The ST viewer requieres also a TSV file with spot coordinates with one of the following formats: SPOT X SPOT Y chip x chip y pixel x pixel Y or SPOT chip x chip y pixel x pixel y or SPOT pixel x pixel y or SPOT X Y Z The first listed format is compatible with the ST Spot Detector and the last format is designed for 3D datasets. For 2D datasets the HE stained image of the tissue section is required. For 3D datasets a 3D Mesh object can be provided. Loading a dataset If you want to load a dataset you can go to the \"Datasets view\" and click in the button \"Import dataset\" then a dialog form will be shown where you can load the matrix of counts, the HE image and other files. You can also upload a dataset automatically if its files ar","default_branch":null,"files":null,"tree":[],"storefront":"/r/jfnavarro","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/jfnavarro/st_viewer/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}