10x Visium spatial transcriptomics data analysis with STdeconvolve ...

I'm trying out different video styles to teach students about bioinformatics analyses for spatially resolved transcriptomics data.

Integrating Single Cell and Visium Spatial Gene Expression Data

Tutorial: Applying CSIDE to Spatial Transcriptomics Data: Multiple regions in Visium with full mode RCTD; Analysis Guide: Integrating 10x Visium and Chromium ...

Live R Coding Session - Spatial transcriptomics data analysis with ...

... spatial transcriptomics Visium dataset from 10X Genomics using STdeconvolve with SpotClean preprocessing. I hope this will help give ...

Exploring Your Visium Data: A Spot Deconvolution Story

Publication Highlight: Benchmarking Methods to Integrate Spatial and Single-cell Transcriptomics Data ... Getting started with 10x data analysis.

Summary | STdeconvolve - JEFworks Lab

Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data. ... This tutorial demonstrates an analysis workflow on 10X ...

MUSTANG: Multi-sample spatial transcriptomics data analysis with ...

(A) Paired anterior-posterior slices placed on the 10X Visium gene expression slides. (B) Spot-based spatial pie charts of MUSTANG-inferred brain region ...

Reference-free cell type deconvolution of multi-cellular pixel ...

a STdeconvolve takes as input a spatial transcriptomics (ST) gene counts ... 10X Visium data of the mouse coronal section of the cortex ...

JEFworks-Lab/STdeconvolve: Reference-free cell-type ... - GitHub

Reference-free cell-type deconvolution of multi-cellular spatially resolved transcriptomics data - JEFworks-Lab/STdeconvolve. ... Analysis of 10X Visium data ...

Flexible Analysis of Spatial Transcriptomics Data (FAST) - bioRxiv

based spatial transcriptomics (e.g., 10X Visium) can provide whole ... For example,. STdeconvolve is a reference-free spatial deconvolution method.

A guidebook of spatial transcriptomic technologies, data resources ...

Several reviews have recently demonstrated the process of spatial transcriptomics data analysis ... For 10X Visium technology, SpaceRanger [63] is designed to ...

Differential gene expression between 10X visium spatial ... - GitHub

I currently have some 10X visium spatial transcriptomics data that I am looking to perform differential gene expression analysis on in different regions of the ...

Computational Strategies and Algorithms for Inferring Cellular ...

While spatially resolved transcriptomics technologies, such as spatial transcriptomics (ST), Slide-seq, 10X Genomics Visium, high-definition ...

MUSTANG: Multi-sample spatial transcriptomics data analysis with ...

Figure 3A shows the four tissue slices placed on the 10X Visium gene expression slides. Due to the presence of nearby brain tissue regions in.

Deconvolution algorithms for inference of the cell-type composition ...

... data and 10X Visium data. As another alternative to ... Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies.

BioTuring Lens: Spatial Deconvolution on Visium Data - YouTube

10x Visium spatial transcriptomics data analysis with STdeconvolve in R Prof. Jean Fan 4.2K views 19:26 Go to channel NEVER install these programs on your PC... ...

A comprehensive comparison on cell type composition inference for ...

... 10X Visium Spatial platform [4, 18]. ... A major barrier in downstream analysis of the 10X Visium data is the resolution of each spot.

A comprehensive comparison on cell-type composition inference for ...

Cell2location performs reasonably well on Spatial Transcriptomics and Visium data when there are a sufficient number of genes. ... For example, in our analysis of ...

CellsFromSpace: a fast, accurate, and reference-free tool to ...

... Visium datasets available from 10x ... Analysis of Visium spatial transcriptomics data using CellsFromSpace's independent component analysis pipeline.

A comprehensive benchmarking with practical guidelines for cellular ...

For the sequencing-based spatial transcriptomics data (ST, Visium ... spatial transcriptomics data analyses. Following our assessment, we ...

single cell spatial transcriptomics data visualization in base R

Live R Coding Session - Spatial transcriptomics data analysis with STdeconvolve ... How to Analyze 10x Visium Spatial Gene Expression Data. Partek ...