E-spatial

Monorail can be used to process local and/or private data, allowing results to be directly compared to any study in recount3. Taken together, Monorail-pipeline tools help biologists maximize the utility of publicly available RNA-seq data, especially to improve their understanding of newly collected data. This is for helping potential users of the Monorail RNA-seq processing pipeline (alignment/quantification) get started running their own data through it.

Understanding global communications among cells requires accurate representation of cell-cell signaling links and effective systems-level analyses of those links. We construct a database of interactions among ligands, receptors and their cofactors that accurately represent known heteromeric molecular complexes. We then develop **CellChat**, a tool that is able to quantitatively infer and analyze intercellular communication networks from single-cell RNA-sequencing (scRNA-seq) data. CellChat predicts major signaling inputs and outputs for cells and how those cells and signals coordinate for functions using network analysis and pattern recognition approaches. Through manifold learning and quantitative contrasts, CellChat classifies signaling pathways and delineates conserved and context-specific pathways across different datasets. Applying **CellChat** to mouse and human skin datasets shows its ability to extract complex signaling patterns.

This notebook illustrates how to convert data from a Seurat object into a Scanpy annotation data and a Scanpy annotation data into a Seurat object using the BioStudio data transformation library (currently under development). It facilitates continued research using libraries that interact with Scanpy in Python and Seurat in R. seurat.to.adata function can retain information about reductions (such as PCA, t-SNE, UMAP and Seurat Clusters) and spatial information.

Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of gene expression at the individual cell level, enabling researchers to uncover heterogeneity and dynamics within complex cellular populations. To analyze and interpret scRNA-seq data effectively, bioinformaticians often rely on specialized tools. In this benchmarking study, we aim to compare the performance of Bioturing Alpha, Scanpy and Seurat in terms of their execution time in various tools of scRNA-seq analysis pipeline. Tools used in scRNA-seq analysis pipeline: - Preprocessing: This step involves tasks such as quality control, filtering out low-quality cells, normalizing gene expression, identifying highly variable genes and regress out unwanted variance. - Linear Dimensionality Reduction: Perform linear dimensionality reduction using techniques such as Principal Component Analysis (PCA) before applying batch effect removal. PCA captures the most significant sources of variation in the data by projecting it onto orthogonal axes. - Batch Effect Removal: Apply batch effect removal methods using Harmony integrate to mitigate the influence of batch effects on downstream analyses. - Clustering: Apply clustering algorithms to partition cells into distinct clusters based on their gene expression profiles. Evaluate the accuracy of cluster assignments by comparing them to known cell types, if available. - Non-Linear Dimensionality Reduction: Utilize non-linear dimensionality reduction techniques, such as t-Distributed Stochastic Neighbor Embedding (t-SNE) and Uniform Manifold Approximation and Projection (UMAP). Apply t-SNE and UMAP to visualize the data in lower-dimensional spaces and assess their ability to reveal intricate cluster patterns.

In this notebook, we present COMMOT (COMMunication analysis by Optimal Transport) to infer cell-cell communication (CCC) in spatial transcriptomic, a package that infers CCC by simultaneously considering numerous ligand–receptor pairs for either spatial transcriptomic data or spatially annotated scRNA-seq data equipped with spatial distances between cells estimated from paired spatial imaging data. A collective optimal transport method is developed to handle complex molecular interactions and spatial constraints. Furthermore, we introduce downstream analysis tools to infer spatial signaling directionality and genes regulated by signaling using machine learning models.

Generative pre-trained models have demonstrated exceptional success in various fields, including natural language processing and computer vision. In line with this progress, scGPT has been developed as a foundational model tailored specifically for the field of single-cell biology. It employs the generative pre-training transformer framework on an extensive dataset comprising more than 33 million cells. scGPT effectively extracts valuable biological insights related to genes and cells and can be fine-tuned to excel in numerous downstream applications.

Single-cell data analysis is revolutionizing biological research, but often these dataset sizes can be massive and pose challenges for submission process. Bioalpha-Biocolab addresses this issue by implementing advanced algorithms and leveraging efficient computational resources to overcome these challenges.

SCENIC Suite is a set of tools to study and decipher gene regulation. Its core is based on SCENIC (Single-Cell Regulatory Network Inference and Clustering) which enables you to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data. pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell Regulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.

This tool provides a user-friendly and automated way to analyze large-scale single-cell RNA-seq datasets stored in RDS (Seurat) format. It allows users to run various analysis tools on their data in one command, streamlining the analysis workflow and saving time. Note that this notebook is only for the demonstration of the tool. Users can run the tool directly through the command line. Currently, we support: - CellChat - Inference and analysis of cell-cell communication using CellChat

In the realm of cancer research, grasping the intricacies of intratumor heterogeneity and its interplay with the immune system is paramount for deciphering treatment resistance and tumor progression. While single-cell RNA sequencing unveils diverse transcriptional programs, the challenge persists in automatically discerning malignant cells from non-malignant ones within complex datasets featuring varying coverage depths. Thus, there arises a compelling need for an automated solution to this classification conundrum. SCEVAN (De Falco et al., 2023), a variational algorithm, is designed to autonomously identify the clonal copy number substructure of tumors using single-cell data. It automatically separates malignant cells from non-malignant ones, and subsequently, groups of malignant cells are examined through an optimization-driven joint segmentation process.

Computational methods that model how the gene expression of a cell is influenced by interacting cells are lacking. We present NicheNet, a method that predicts ligand–target links between interacting cells by combining their expression data with prior knowledge of signaling and gene regulatory networks. We applied NicheNet to the tumor and immune cell microenvironment data and demonstrated that NicheNet can infer active ligands and their gene regulatory effects on interacting cells.

The recent development of experimental methods for measuring chromatin state at single-cell resolution has created a need for computational tools capable of analyzing these datasets. Here we developed Signac, a framework for the analysis of single-cell chromatin data, as an extension of the Seurat R toolkit for single-cell multimodal analysis. **Signac** enables an end-to-end analysis of single-cell chromatin data, including peak calling, quantification, quality control, dimension reduction, clustering, integration with single-cell gene expression datasets, DNA motif analysis, and interactive visualization. Furthermore, Signac facilitates the analysis of multimodal single-cell chromatin data, including datasets that co-assay DNA accessibility with gene expression, protein abundance, and mitochondrial genotype. We demonstrate scaling of the Signac framework to datasets containing over 700,000 cells.

Many spatially resolved transcriptomic technologies do not have single-cell resolution but measure the average gene expression for each spot from a mixture of cells of potentially heterogeneous cell types. Here, we introduce a deconvolution method, conditional autoregressive-based deconvolution (CARD), that combines cell-type-specific expression information from single-cell RNA sequencing (scRNA-seq) with correlation in cell-type composition across tissue locations. Modeling spatial correlation allows us to borrow the cell-type composition information across locations, improving accuracy of deconvolution even with a mismatched scRNA-seq reference. **CARD** can also impute cell-type compositions and gene expression levels at unmeasured tissue locations to enable the construction of a refined spatial tissue map with a resolution arbitrarily higher than that measured in the original study and can perform deconvolution without an scRNA-seq reference. Applications to four datasets, including a pancreatic cancer dataset, identified multiple cell types and molecular markers with distinct spatial localization that define the progression, heterogeneity and compartmentalization of pancreatic cancer.

Spatial transcriptomics (ST) technology has allowed to capture of topographical gene expression profiling of tumor tissues, but single-cell resolution is potentially lost. Identifying cell identities in ST datasets from tumors or other samples remains challenging for existing cell-type deconvolution methods. Spatial Cellular Estimator for Tumors (SpaCET) is an R package for analyzing cancer ST datasets to estimate cell lineages and intercellular interactions in the tumor microenvironment. Generally, SpaCET infers the malignant cell fraction through a gene pattern dictionary, then calibrates local cell densities and determines immune and stromal cell lineage fractions using a constrained regression model. Finally, the method can reveal putative cell-cell interactions in the tumor microenvironment. In this notebook, we will illustrate an example workflow for cell type deconvolution and interaction analysis on breast cancer ST data from 10X Visium. The notebook is inspired by SpaCET's vignettes and modified to demonstrate how the tool works on BioTuring's platform.

Droplet-based single-cell RNA sequence analyses assume that all acquired RNAs are endogenous to cells. However, there is a certain amount of cell-free mRNAs floating in the input solution (referred to as 'the soup'), created from cells in the input solution being lysed. These background mRNAs are then distributed into the droplets with cells and sequenced alongside them, resulting in background contamination that confounds the biological interpretation of single-cell transcriptomic data. SoupX (Young and Behjati, 2020) is one of the methods proposed for ambient mRNA removal. In this notebook, we will illustrate a workflow example that applies SoupX to correct the ambient RNA in a dataset of 10k PBMC cells. The output of SoupX is a modified counts matrix, which can be used for any downstream analysis tool.