CellChat

Single-cell RNA sequencing (scRNA-seq) protocols often face challenges in measuring the expression of all genes within a cell due to various factors, such as technical noise, the sensitivity of scRNA-seq techniques, or sample quality. This limitation gives rise to a need for the prediction of unmeasured gene expression values (also known as dropout imputation) from scRNA-seq data. ADImpute (Leote A, 2023) is an R package combining several dropout imputation methods, including two existing methods (DrImpute, SAVER), two novel implementations: Network, a gene regulatory network-based approach using gene-gene relationships learned from external data, and Baseline, a method corresponding to a sample-wide average.. This notebook is to illustrate an example workflow of ADImpute on sample datasets loaded from the package. The notebook content is inspired from ADImpute's vignette and modified to demonstrate how the tool works on BioTuring's platform.

Single-cell RNA sequencing (scRNA-seq) data have allowed us to investigate cellular heterogeneity and the kinetics of a biological process. Some studies need to understand how cells change state, and corresponding genes during the process, but it is challenging to track the cell development in scRNA-seq protocols. Therefore, a variety of statistical and computational methods have been proposed for lineage inference (or pseudotemporal ordering) to reconstruct the states of cells according to the developmental process from the measured snapshot data. Specifically, lineage refers to an ordered transition of cellular states, where individual cells represent points along. pseudotime is a one-dimensional variable representing each cell’s transcriptional progression toward the terminal state. Slingshot which is one of the methods suggested for lineage reconstruction and pseudotime inference from single-cell gene expression data. In this notebook, we will illustrate an example workflow for cell lineage and pseudotime inference using Slingshot. The notebook is inspired by Slingshot's vignette and modified to demonstrate how the tool works on BioTuring's platform.

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

Build single-cell trajectories with the software that introduced **pseudotime**. Find out about cell fate decisions and the genes regulated as they're made. Group and classify your cells based on gene expression. Identify new cell types and states and the genes that distinguish them. Find genes that vary between cell types and states, over trajectories, or in response to perturbations using statistically robust, flexible differential analysis. In development, disease, and throughout life, cells transition from one state to another. Monocle introduced the concept of **pseudotime**, which is a measure of how far a cell has moved through biological progress. Many researchers are using single-cell RNA-Seq to discover new cell types. Monocle 3 can help you purify them or characterize them further by identifying key marker genes that you can use in follow-up experiments such as immunofluorescence or flow sorting. **Single-cell trajectory analysis** shows how cells choose between one of several possible end states. The new reconstruction algorithms introduced in Monocle 3 can robustly reveal branching trajectories, along with the genes that cells use to navigate these decisions.