Standard Apps

Standard Apps in PanHunter are core components that are available across all projects by default. They provide essential functionalities for data exploration and analysis and are designed to be universally applicable regardless of the dataset.

The below is a list of standard apps provided by PanHunter:

Sample QC App

The Sample QC app is utilised to ensure sample quality, with an emphasis on RNA-seq and similar platforms. The application presents data supplied by the STAR aligner tool, Samtools, and the HTSeq package.

For more information go to Sample QC app page.

Proteomics QC App

The Proteomics QC app is a comprehensive tool designed to streamline and enhance quality control processes in proteomics research. It offers features for assessing data integrity, identifying anomalies, and ensuring the reliability of protein analysis results.

For more information go to Proteomics QC app page.

Project Overview App

Projects in transcriptomics can hold multiple studies, aggregating data from different experiments. This allows to compare data generated on different technology platforms, different protocols and different biological systems. The Project Overview app provides an overview of the data sets with the current project.

For more information go to Project Overview app page.

scExplorer App

The scExplorer app is mainly used to visualize single cell rna seq data and to annotate different cell types.

For more information go to scExplorer app page.

New Comparison App

The New Comparison app is used to visualize samples and create top tables of differentially expressed genes, following a comparison of specific sample groups (for instance, representing distinct treatments). The resulting tables can then be reviewed with the Top Tables application.

For more information go to New Comparison app page.

Comparisons App

The Comparisons app is used to inspect and compare tables of differentially expressed genes as generated in the New Comparisons app.

For more information go to Comparisons app page.

MA Plot App

The MA Plot app is used to visualize and inspect the log fold changes (M) vs. average expression levels of the contrast denominator (A) for genes from two Comparisons (refer TopTables app).

For more information go to MA Plot app page.

Gene Info App

The gene info app provides all available information regarding a single gene of interest.

For more information go to Gene info app page.

Gene Comparison App

The Gene Comparison app provides a heatmap visualization of average expression levels similar to the gene info app, but for multiple selected genes.

For more information go to Gene Comparison app page.

Gene Clustering App

The Gene Clustering app aims to identify co-expressed or co-regulated genes for a single selected gene.

For more information go to Gene Clustering app page.

TF Targets App

The TF Targets app provides a user-friendly platform for exploring the intricate network of transcription factors (TFs) and their target genes.

For more information go to TF Targets app page.

Pathway Mapping App

The Pathway Mapping app was designed to visualize and quickly compare fold change values of genes present in one or two top tables in the context of organism-specific pathway maps.

For more information go to Pathway Mapping app page.

Network Visualization App

The network visualization app provides an interactive visualization of top table genes in the context of gene and protein interaction networks.

For more information go to Network Visualization app page.

Signature Visualization App

The Signature Visualization app provides an interactive visualization of a signature against the top table genes.

For more information go to Signature Visualization app page.

Enrichment Visualization App

The Enrichment visualisation app enables conducting enrichment analysis for a provided dataset top table, an individual comparison from a comparison group or a manually entered feature (gene) list with user-defined parameters, and obtaining a visualisation of the analysis findings.

For more information go to Enrichment Visualization app page.

scDeepDive App

The scDeepDive app enables visualization and cell type annotation of single-cell RNA-seq data using machine learning–based reference mapping or manual marker-based approaches.

For more information go to scDeepDive app page.

Transcriptomics QC App

The Transcriptomics QC app is used to inspect and assess quality control metrics for bulk and plate-based RNA-seq data.

For more information go to Transcriptomics QC app page.

Data Overview App

The Data Overview app provides a centralized view to explore, organize, and manage all data associated with a project.

For more information go to Data Overview app page.