Clinical Trials To Pubmed

The Clinical Trials and PubMed Article Search application is a powerful web-based platform that offers two main interconnected functionalities:

1. Clinical Trials Search:

Users can search for clinical trials using four different methods:

• NCT ID (direct trial lookup)
• Term-based search
• Condition-based search (e.g., “diabetes”, “cancer”)
• Intervention-based search (e.g., specific drugs or treatments)

The search results display in a table format showing trial ID, title, conditions, and a …

CSRP P50

Center for Suicide Research and Prevention https://csrp.mgh.harvard.edu/

Exploration of pre-computed knowledge graphs on mental health related populations.

Authors: Thomas Charlon, Enci Cai, Clara-Lea Bonzel, Tianxi Cai

Dictionary: Mass General Brigham Codebook

[Password protected app]

Mass General Brigham dictionary with semantic search capability (fine-tuned BGE).

1.4M local codes of 4 types (diagnoses, medications, laboratory tests, procedures), mapped to common ontologies (ICD, RXNORM, LOINC, CPT/ICDPCS) and group codes (Phecodes, RXNORM ingrediente, higher-level LOINC, CCS).

Knowledge Graphs

Knowledge graphs enable to efficiently visualize and gain insights into large-scale data analysis results, as p-values from multiple studies or embedding data matrices. The usual workflow is a user providing a data frame of association studies results and specifying target nodes, e.g. phenotypes, to visualize. The knowledge graph then shows all the features which are significantly associated with the phenotype, with the edges being proportional to the association scores. As the user adds several …

Word Embeddings In Mental Health (R in Medicine, 2024)

This suicide prevention workshop, developed with Veterans Affairs, aims to assist clinicians by analyzing health data to improve follow-up with at-risk patients, enable access to relevant notes, and share insights while preserving confidentiality. It covers the project overview, the Diagnostic Manual’s role, a proposed diagnosis, an analysis of suicide publications, and instructions for reproducing the work - all to leverage data and expertise for suicide prevention, especially for …

Introducing The Organization Of A Project Git Repository

Example on project CSRP P50 (Center for Suicide Research and Prevention https://csrp.mgh.harvard.edu/)

Overall structure and collaborative development

Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations

Single nucleotide polymorphisms are the most common genetic variations in humans and genome-wide microarrays measure up to several millions. Physically close polymorphisms often exhibit correlation structures and are said to be in linkage disequilibrium when they are more correlated than randomly expected. The snplinkage package provides linkage disequilibrium visualizations by displaying correlation matrices annotated with chromosomic positions and gene names. Two types of displays are provided …

OPTICS K-Xi Density-Based Clustering

Density-based clustering methods are well adapted to the clustering of high-dimensional data and enable the discovery of core groups of various shapes despite large amounts of noise. This package provides a novel density-based cluster extraction method, OPTICS k-Xi, and a framework to compare k-Xi models using distance-based metrics to investigate datasets with unknown number of clusters. The vignette first introduces density-based algorithms with simulated datasets, then presents and evaluates …

opticskxi: OPTICS K-Xi Density-Based Clustering

Density-based clustering methods are well adapted to the clustering of high-dimensional data and enable the discovery of core groups of various shapes despite large amounts of noise. This package provides a novel density-based cluster extraction method, OPTICS k-Xi, and a framework to compare k-Xi models using distance-based metrics to investigate datasets with unknown number of clusters. The vignette first introduces density-based algorithms with simulated datasets, then presents and evaluates …

nlpembeds: Natural Language Processing Embeddings

Provides efficient methods to compute co-occurrence matrices, pointwise mutual information (PMI) and singular value decomposition (SVD). In the biomedical and clinical settings, one challenge is the huge size of databases, e.g. when analyzing data of millions of patients over tens of years. To address this, this package provides functions to efficiently compute monthly co-occurrence matrices, which is the computational bottleneck of the analysis, by using the ‘RcppAlgos’ package and …

kgraph: Knowledge Graphs Constructions and Visualizations

Knowledge graphs enable to efficiently visualize and gain insights into large-scale data analysis results, as p-values from multiple studies or embedding data matrices. The usual workflow is a user providing a data frame of association studies results and specifying target nodes, e.g. phenotypes, to visualize. The knowledge graph then shows all the features which are significantly associated with the phenotype, with the edges being proportional to the association scores. As the user adds several …

linevis: Interactive Time Series Visualizations

Create interactive time series visualizations. ’linevis’ includes an extensive API to manipulate time series after creation, and supports getting data out of the visualization. Based on the ’timevis’ package and the ‘vis.js’ Timeline ‘JavaScript’ library https://visjs.github.io/vis-timeline/docs/graph2d/.

snplinkage: Single Nucleotide Polymorphisms Linkage Disequilibrium Visualizations

Linkage disequilibrium visualizations of up to several hundreds of single nucleotide polymorphisms (SNPs), annotated with chromosomic positions and gene names. Two types of plots are available for small numbers of SNPs (<40) and for large numbers (tested up to 500). Both can be extended by combining other ggplots, e.g. association studies results, and functions enable to directly visualize the effect of SNP selection methods, as minor allele frequency filtering and TagSNP selection, with a …

sgraph: Network Visualization Using 'sigma.js'

Sgraph enables to visualize graphs using the latest stable version of Sigma.js v2.4.0. Graphs are created using the igraph package.

This package uses ggplot-like grammar: a basic visualization is first created and then modified by adding/removing attributes with additional functions, using the pipe operator from the magrittr package.

OPTICS K-Xi vignette 2: Ensemble Metrics And Models For Density-Based Clustering (CRAN, 2025)

The OPTICS k-Xi density-based clustering pipeline now integrates ensemble metrics which enable to increase the stability of the clusters and the reproducibility of the results on evaluation datasets. Up to now, OPTICS k-Xi computed several distance-based metrics but did not implement any way of merging together their results, it was up to the user to select the most relevant metric or to merge them together. Recently, we applied the pipeline on natural language processing embeddings and the …

Co-occurrence Matrices and PMI-SVD Embeddings (CRAN, 2025)

The nlpembeds package provides efficient methods to compute co-occurrence matrices, pointwise mutual information (PMI) and singular value decomposition (SVD) embeddings. In the biomedical and clinical setting, one challenge is the huge size of databases of electronic health records (EHRs), e.g. when analyzing data of millions of patients over tens of years. To address this, this package provides functions to efficiently compute monthly co-occurrence matrices, which is the computational …

Knowledge Graphs (CRAN, 2024)

Knowledge graphs enable to organize vast amounts of knowledge and has been used extensively on internet to help websites share data and integrate one another. In the domain of research and knowledge discovery, they enable to organise results and provide specific views of results by showing subsets of interest.

SNPLinkage vignette 2: Other Data Formats And Customizations (CRAN, 2024)

SNPLinkage is modular enough to use directly dataframes of correlation matrices and chromosomic positions specified by the user, e.g. for visualizing RNASeq data. The user can compute a correlation matrix or any kind of pair-wise similarity matrix independently and then use SNPLinkage to build and arrange easily customizable ggplot2 objects.

Single Nucleotide Polymorphism Linkage Disequilibrium Visualizations (CRAN, 2023)

Single nucleotide polymorphisms are the most common genetic variations in humans and genome-wide microarrays measure up to several millions. Physically close polymorphisms often exhibit correlation structures and are said to be in linkage disequilibrium when they are more correlated than randomly expected. The snplinkage package provides linkage disequilibrium visualizations by displaying correlation matrices annotated with chromosomic positions and gene names. Two types of displays are provided …

Genetic clustering for the discovery of a new classification of systemic autoimmune diseases (PhD, 2019)

Systemic autoimmune diseases are considered to share genetic susceptibility markers and clinicians expect treatments could benefit from a molecular-based reclassification. In that objective, more than 1,000 patients were recruited by the PRECISESADS project to measure their genotypes and their proteins concentrations in blood.

OPTICS K-Xi Density-Based Clustering (CRAN, 2019)

Density-based clustering methods are well adapted to the clustering of high-dimensional data and enable the discovery of core groups of various shapes despite large amounts of noise. The opticskxi R package provides a novel density-based cluster extraction method, OPTICS k-Xi, and a framework to compare k-Xi models using distance-based metrics to investigate datasets with unknown number of clusters. This article ␜rst introduces density-based algorithms with simulated datasets, then presents and …

Replication of the principal component analyses of the human genome diversity panel (F1000Research, 2017)

Background. In 2008, several principal component analyses (PCAs) applied on 660,918 single-nucleotide polymorphisms (SNPs) from 938 individuals from 51 worldwide populations of the Human Genome Diversity Panel were published by Li et al. PCAs were applied on subsets of individuals sharing a common geographic origin and showed that in several geographic regions, genome-wide variations of SNPs grouped individuals by populations in the two first principal components. In this study, we replicated …

Single nucleotide polymorphism clustering in systemic autoimmune diseases (PLOSOne, 2016)

Systemic Autoimmune Diseases, a group of chronic inflammatory conditions, have variable symptoms and difficult diagnosis. In order to reclassify them based on genetic markers rather than clinical criteria, we performed clustering of Single Nucleotide Polymorphisms. However naive approaches tend to group patients primarily by their geographic origin. To reduce this “ancestry signal”, we developed SNPClust, a method to select large sources of ancestry-independent genetic variations from all …