Software

Microenvironmental heterogeneity parallels breast cancer progression: A histology-genomics integration analysis
Natrajan R, Sailem H, Mardakheh FM, Arias MG, Dowsett M, Bakal C, Yuan Y*
PLOS Medicine (2016) [Sweave; R package beta version]

We propose a clinically relevant role of tumour microenvironmental diversity for advanced breast tumors and highlight that ecological statistics can be translated into medical advances for identifying new biomarkers and for understanding the synergistic interplay between the microenvironment and cancer genomics.

Cancer-immune hotspots
Statistically significant clusters of cancer and immune cells

Modern Pathology, 2015 [Sweave]

Following image analysis to identify and locate cancer and immune cells in H&E-stained breast tumour samples, we can test for spatial clustering between these cells by applying Getis-Ord Gi*, a tool commonly used in demographics and crime mapping.

FISHalyseR
Automated fluorescence in situ hybridization analysis in R

Bioconductor Package [PDF; R Package]

FISHalyseR is a highthroughput tool for quantitative analysis of molecular heterogeneity at 
single-cell resolution in FISH images with an unlimited number of probes.

ITLR
Intra-Tumour Lymphocyte Ratio

Journal of the Royal Society Interface [Sweave]

ITLR is a fully automated, computer-assisted method for scoring intratumour lymphocytes in histology samples with the fusion of high-throughput image processing and robust statistical analysis.

CRImage
Histopathology H&E image processing

Science Translational Medicine, 2012 [ PDF; Supplement; R package; Sweave; Data and code for Sweave; Lay-description ]

CRImage provides image analysis tools for segmentation and classification of various cell types in H&E images. The package also comes with an efficient algorithm for copy-number data correction based on the unbiased estimates of tumours cellularity from the image analysis.

PSDF
Integrative clustering with Dirichlet Process for subtype discovery

PLoS Comp Bio 2011 [PDF; Matlab code]

PSDF is a Bayesian non-parametric graphical model for patient-specific data fusion, which assigns subtypes by choosing patient-specific features from both genomic and transcriptomic data, and therefore informs both subtype classification and potential personalized treatment targets.

DANCE
Dissecting regulatory heterogeneity in disease subtypes

Bioinformatics 2011 [PDF; R package]

DANCE is a penalized model for characterizing how DNA alterations lead to gene deregulation at the RNA level in a subtype-specific context, characterizing oncogene activation or tumour suppressor loss contributing to pathogenesis.

lol
Sparse reconstruction of DNA-RNA interaction networks

IEEE/ACM Trans Comp Bio Bioinfo 2011 [PDF; R package]

lol was specifically designed for multicollinear predictor variables, and therefore is particularly suitable for association study to delineate the trans-regulation relations between DNA copy number aberrations and RNA expression levels.

DPC
Directed Partial Correlation for efficient large-scale gene network inference

PLoS ONE 2011 [PDF; R package; data]

DPC provides an efficient solution to large-scale transcriptional regulatory network inference. It combines the efficiency of partial correlation for setting up the network topology, and the concept of Granger causality to eliminate indirect regulations.

CRImage installation how-to

- A step-by-step guide for Mac OS

In response to a recent update of EBImage, we have produced a new version of CRImage for 64bits. To install CRImage you need the EBImage R package, which requires: X11,ImageMagick, GTK+(optional). Here is an example step-by-step guide to install CRImage on Mac OS.

Alternatively, you can use fink to install most dependencies of EBImage and CRImage.

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lol

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FISHalyseR

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