Statistical Web Applications

A range of applications have been developed to allow interactive exploration and analytics of large omics datasets. Any difficulties using an application? Let us know about them.

Single-cell analysis

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CiteFuse

A suite of tools for pre-processing, clustering, differential RNA and ADT expression analysis, ligand-receptor interaction analysis of CITE-seq data.

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scClassify

Single cell classification of cell-type hierarchies based on ensemble learning and sample size estimation.

spicyR

Analysis of immunofluorescence, mass cytometry imaging and other assays that can deeply phenotype individual cells and their spatial location.

lisaClust

Identification and visualisation of tissue microenvironments and regions of tissue where spatial associations between cell-types is similar.

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SimBench

A benchmark study of simulation methods for single-cell RNA sequencing data.

COVID-19 Cell Interaction Logo
COVID-19 Cell Interaction

Between-cell-type communication for prediction of COVID-19 disease severity.



Proteomics & Metabolomics

KinasePA
KinasePA

Enables analysis of kinase perturbation experiments..

ClueR
ClueR

Use of prior knowledge to cluster time series proteomics data.

QPEP

A benchmarking scoreboard and visual analytics tools for methods which affect proteomics quantitation.

QCMAP
Mass Spectrometry QC (QCMAP)

Quality control for Mass Spectrometry.

Hierarchical approach to RUV normalisation (hRUV)

Normalisation for large-scale data.



Genomics & Transcriptomics

PACMEN
PACMEN

A tool for exploring the relationships between mutations and gene expression changes in protein interaction subnetworks for 19 tissues analysed by TCGA. R function to produce your own PACMEN input found here.

classifyR
MelanomaExplorer

Enables customised classification, scatterplots of pairs of variables, network visualisations, and survival analysis for a variety of publicly available melanoma datasets.

Heliocidaris erythrogramma Time Series Viewer

Quick and easy time-series plots of gene expression of a particular sea urching gene expression dataset.

bcGST
bcGST: Bias-Corrected Gene Set Test

Gene set test method for boutique arrays.

arrayQuality

Quality control for Microarray Datasets.

CPOP
Cross-Platform Omics Prediction (CPOP)

A statistical machine learning framework for wider implementation of precision medicine