E-spatial

Geneformer is a foundation transformer model pretrained on a large-scale corpus of ~30 million single cell transcriptomes to enable context-aware predictions in settings with limited data in network biology. Here, we will demonstrate a basic workflow to work with ***Geneformer*** models. These notebooks include the instruction to: 1. Prepare input datasets 2. Finetune Geneformer model to perform specific task 3. Using finetuning models for cell classification and gene classification application

Doublets are a characteristic error source in droplet-based single-cell sequencing data where two cells are encapsulated in the same oil emulsion and are tagged with the same cell barcode. Across type doublets manifest as fictitious phenotypes that can be incorrectly interpreted as novel cell types. DoubletDetection present a novel, fast, unsupervised classifier to detect across-type doublets in single-cell RNA-sequencing data that operates on a count matrix and imposes no experimental constraints. This classifier leverages the creation of in silico synthetic doublets to determine which cells in the input count matrix have gene expression that is best explained by the combination of distinct cell types in the matrix. In this notebook, we will illustrate an example workflow for detecting doublets in single-cell RNA-seq count matrices.

PopV uses popular vote of a variety of cell-type transfer tools to classify cell-types in a query dataset based on a test dataset. Using this variety of algorithms, they compute the agreement between those algorithms and use this agreement to predict which cell-types have a high likelihood of the same cell-types observed in the reference.

The development of immune checkpoint-based immunotherapies has been a major advancement in the treatment of cancer, with a subset of patients exhibiting durable clinical responses. A predictive biomarker for immunotherapy response is the pre-existing T-cell infiltration in the tumor immune microenvironment (TIME). Bulk transcriptomics-based approaches can quantify the degree of T-cell infiltration using deconvolution methods and identify additional markers of inflamed/cold cancers at the bulk level. However, bulk techniques are unable to identify biomarkers of individual cell types. Although single-cell RNA sequencing (scRNAseq) assays are now being used to profile the TIME, to our knowledge there is no method of identifying patients with a T-cell inflamed TIME from scRNAseq data. Here, we describe a method, iBRIDGE, which integrates reference bulk RNAseq data with the malignant subset of scRNAseq datasets to identify patients with a T-cell inflamed TIME. Utilizing two datasets with matched bulk data, we show iBRIDGE results correlated highly with bulk assessments (0.85 and 0.9 correlation coefficients). Using iBRIDGE, we identified markers of inflamed phenotypes in malignant cells, myeloid cells, and fibroblasts, establishing type I and type II interferon pathways as dominant signals, especially in malignant and myeloid cells, and finding the TGFβ-driven mesenchymal phenotype not only in fibroblasts but also in malignant cells. Besides relative classification, per-patient average iBRIDGE scores and independent RNAScope quantifications were utilized for threshold-based absolute classification. Moreover, iBRIDGE can be applied to in vitro grown cancer cell lines and can identify the cell lines that are adapted from inflamed/cold patient tumors.