Single Cell Data Analysis
Made Easy with Trailmaker

Flexible Data Entry and Exit Points

Trailmaker provides end-to-end analysis of Evercode WT data with flexibility built in to support count matrices from various single-cell technologies. Advanced analysis is enabled through Seurat object download for code-based methods.

FASTQ File Processing

Trailmaker’s Pipeline module processes Parse Biosciences EvercodeTM WT FASTQ files, generating reports and count matrices for viewing or downloading.

Data is automatically sent to the Insights module for downstream processing and visualization.

In-Depth Filtering and QC

You are guided step-by-step through the necessary filtering and integration processes.

Automatically determined default settings deliver ready-to-explore data analysis, with user friendly controls for adjusting filtering thresholds, parameters and methods.

Automatic Cell Type Annotation

Automated cell type prediction is provided using the ScType algorithm that’s built on an extensive database of cell population markers across tissues and species.

Gene Expression

• Search for genes of interest and view expression on a UMAP or t-SNE plot in a single click
• Violin plots make it easy to visualize gene expression across clusters, samples or groups
• View gene sets of interest in dot plots or heatmaps

Custom cell set generation

If Leiden or Louvain clusters don’t quite fit your use case, you can generate custom cell sets using the lasso or gene expression features. It’s also easy to combine clusters or to subset specific clusters into a new analysis.

Differential Expression Analysis

Differential expression analysis calculates the differences in gene expression profiles between clusters or cell populations of interest.

Differential expression results can be filtered, plotted in a Volcano plot, sent for pathway analysis and downloaded.

Fully Customizable Publication-Ready Plots

Pre-loaded plots are available to view, customize and download.

Customization options include:

• Specify genes, cell sets and samples/groups to be plotted
• Adjust plot size, axes labels, ranges, sizes, and font
• Specify the title and legend values and location
• Define the colour scheme
• Export the data (CSV file) and plot (SVG or PNG image file)

Trajectory Analysis

Calculate trajectories using the Monocle3 algorithm and plot pseudotime in a customizable trajectory plot.

Data Sharing

Share individual projects with colleagues or collaborators to work together on data analysis.

Datasets Repository

Grab a dataset from the Trailmaker datasets repository to start exploring Trailmaker’s data analysis and visualization capabilities today!