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TBEL Data Science Resource List

  • bgtaylor1
  • Dec 11, 2024
  • 2 min read

Provided by Liang Li and Lulu Shang.

If you need further assistance, contact TBEL-CDMC@mdanderson.org.


Task

Approach

Tools

Applications

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Quality control

SpotClean

Quality control of spatial transcriptomics data, removing ambient RNA contamination.


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Batch effect removal

Harmony, ComBat, BBKNN

Correcting batch effects across datasets.


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DE analysis

Wilcoxon test in Seurat, RegionalST

Identifying differentially expressed genes across spatial regions or cell types.

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Gene set enrichment analysis

GSEA, gProfiler, fgsea, clusterProfiler, EnrichR

Functional enrichment analysis for spatially resolved genes to identify biological pathways.


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Gene regulatory network

SCENIC, GRNBoost2, GENIE3

Inferring regulatory networks to identify regulatory relationships.


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Deconvolution

Cell2location, RCTD, CARD, SpatialDWLS,

BayesPrism

Deconvolution of SRT data using paired scRNA-seq data.


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CNV inference

SpatialInferCNV, SPATA

Inference of CNVs from SRT data


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Cell-cell interaction

COMMOT, NCEM, NicheDE, NicheNet

Inference of cellular interactions from SRT data


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Cell type annotation

SingleR, scType, Seurat

Annotating cell types based on reference datasets or marker gene expression.


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Neighborhood analysis

Squidpy, Giotto, SpaOTsc

Understanding spatial relationships and clustering between cell types and tissue regions.

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Dimension reduction

SpatialPCA, PRECAST, PCA, NMF

Spatially aware dimension reduction and embedding for downstream analysis


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Spatial domain detection

BayesSpace, Louvain (Seurat), SpaGCN, BASS

Identifying spatial domains and tissue structures using spatial relationships and gene expression.


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Spatially variable genes detection

SPARK, SPARK-X, nnSVG, CELINA

Detecting genes with significant spatial expression patterns, including cell type-specific patterns.


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Multi-omics integration

SpatialGLUE, MOFA+, StabMap

Integrating spatial multi-omics data for comprehensive biological insights.

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Trajectory analysis

Monocle3, Slingshot, STREAM

Analyzing developmental trajectories or pseudotime.


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Data visualization

SpatialView, Seurat, Scanpy, Squidpy, Circos

Visualization of spatial transcriptomics data in 2D/3D contexts.


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Imputation and Alignment

CytoSPACE, Tangram, CellTrek, PASTA

Mapping single-cell RNA-seq data onto spatial data for alignment and high-resolution insights.


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Power analysis and sample size

PoweREST

Calculating statistical power and determining sample size for spatial transcriptomics studies.


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Cell segmentation

Baysor, SCS, DeepCell, Cellpose, StarDist

Identifying and segmenting individual cells or nuclei from spatial images.

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Morphology integration

SpaGCN, iStar, METI

Integrating morphological information from H&E images with spatial transcriptomics.

 

 




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