TFTF: An R-Based Integrative Tool for Decoding Human Transcription Factor-Target Interactions.

Transcription factors (TFs) are crucial in modulating gene expression and sculpting cellular and organismal phenotypes. The identification of TF-target gene interactions is pivotal for comprehending molecular pathways and disease etiologies but has been hindered by the demanding nature of traditional experimental approaches. This paper introduces a novel web application and package utilizing the R program, which predicts TF-target gene relationships and vice versa. Our application integrates the predictive power of various bioinformatic tools, leveraging their combined strengths to provide robust predictions. It merges databases for enhanced precision, incorporates gene expression correlation for accuracy, and employs pan-tissue correlation analysis for context-specific insights. The application also enables the integration of user data with established resources to analyze TF-target gene networks. Despite its current limitation to human data, it provides a platform to explore gene regulatory mechanisms comprehensively. This integrated, systematic approach offers researchers an invaluable tool for dissecting the complexities of gene regulation, with the potential for future expansions to include a broader range of species.

Assessing the distortions introduced when calculating d': A simulation approach.

The discriminability measure d ' is widely used in psychology to estimate sensitivity independently of response bias. The conventional approach to estimate d ' involves a transformation from the hit rate and the false-alarm rate. When performance is perfect, correction methods must be applied to calculate d ' , but these corrections distort the estimate. In three simulation studies, we show that distortion in d ' estimation can arise from other properties of the experimental design (number of trials, sample size, sample variance, task difficulty) that, when combined with application of the correction method, make d ' distortion in any specific experiment design complex and can mislead statistical inference in the worst cases (Type I and Type II errors). To address this problem, we propose that researchers simulate d ' estimation to explore the impact of design choices, given anticipated or observed data. An R Shiny application is introduced that estimates d ' distortion, providing researchers the means to identify distortion and take steps to minimize its impact.

APIS: an updated parentage assignment software managing triploids induced from diploid parents.

In aquaculture, sterile triploids are commonly used for production as sterility gives them potential gains in growth, yields and quality. However, they cannot be reproduced, and DNA parentage assignment to their diploid or tetraploid parents is required to estimate breeding values for triploid phenotypes. No publicly available software has the ability to assign triploids to their parents. Here, we updated the R package APIS to support triploids induced from diploid parents. First, we created new exclusion and likelihood tables that account for the double allelic contribution of the dam and the recombination that can occur during female meiosis. As the effective recombination rate of each marker with the centromere is usually unknown, we set it at 0.5 and found that this value maximises the assignment rate even for markers with high or low recombination rates. The number of markers needed for a high true assignment rate did not strongly depend on the proportion of missing parental genotypes. The assignment power was however affected by the quality of the markers (minor allele frequency, call rate). Altogether, 96 to 192 SNPs were required to have a high parentage assignment rate in a real rainbow trout dataset of 1232 triploid progenies from 288 parents. The likelihood approach was more efficient than exclusion when the power of the marker set was limiting. When more markers were used, exclusion was more advantageous, with sensitivity reaching unity, very low False Discovery Rate (<0.01) and excellent specificity (0.96-0.99). Thus, APIS provides an efficient solution to assign triploids to their diploid parents.

Steroid-tacrolimus drug-drug interaction and the effect of CYP3A genotypes.

AIMS: Tacrolimus, metabolized by CYP3A4 and CYP3A5 enzymes, is susceptible to drug-drug interactions (DDI). Steroids induce CYP3A genes to increase tacrolimus clearance, but the effect is variable. We hypothesized that the extent of the steroid-tacrolimus DDI differs by CYP3A4/5 genotypes. METHODS: Kidney transplant recipients (n = 2462) were classified by the number of loss of function alleles (LOF) (CYP3A5*3, *6 and *7 and CYP3A4*22) and steroid use at each tacrolimus trough in the first 6 months post-transplant. A population pharmacokinetic analysis was performed by nonlinear mixed-effect modelling (NONMEM) and stepwise covariate modelling to define significant covariates affecting tacrolimus clearance. A stochastic simulation was performed and translated into a Shiny application with the mrgsolve and Shiny packages in R. RESULTS: Steroids were associated with modestly higher (3%-11.8%) tacrolimus clearance. Patients with 0-LOF alleles receiving steroids showed the greatest increase (11.8%) in clearance compared to no steroids, whereas those with 2-LOFs had a negligible increase (2.6%) in the presence of steroids. Steroid use increased tacrolimus clearance by 5% and 10.3% in patients with 1-LOF and 3/4-LOFs, respectively. CONCLUSIONS: Steroids increase the clearance of tacrolimus but vary slightly by CYP3A genotype. This is important in individuals of African ancestry who are more likely to carry no LOF alleles, may more commonly receive steroid treatment, and will need higher tacrolimus doses.

SurvdigitizeR: an algorithm for automated survival curve digitization.

BACKGROUND: Decision analytic models and meta-analyses often rely on survival probabilities that are digitized from published Kaplan-Meier (KM) curves. However, manually extracting these probabilities from KM curves is time-consuming, expensive, and error-prone. We developed an efficient and accurate algorithm that automates extraction of survival probabilities from KM curves. METHODS: The automated digitization algorithm processes images from a JPG or PNG format, converts them in their hue, saturation, and lightness scale and uses optical character recognition to detect axis location and labels. It also uses a k-medoids clustering algorithm to separate multiple overlapping curves on the same figure. To validate performance, we generated survival plots form random time-to-event data from a sample size of 25, 50, 150, and 250, 1000 individuals split into 1,2, or 3 treatment arms. We assumed an exponential distribution and applied random censoring. We compared automated digitization and manual digitization performed by well-trained researchers. We calculated the root mean squared error (RMSE) at 100-time points for both methods. The algorithm's performance was also evaluated by Bland-Altman analysis for the agreement between automated and manual digitization on a real-world set of published KM curves. RESULTS: The automated digitizer accurately identified survival probabilities over time in the simulated KM curves. The average RMSE for automated digitization was 0.012, while manual digitization had an average RMSE of 0.014. Its performance was negatively correlated with the number of curves in a figure and the presence of censoring markers. In real-world scenarios, automated digitization and manual digitization showed very close agreement. CONCLUSIONS: The algorithm streamlines the digitization process and requires minimal user input. It effectively digitized KM curves in simulated and real-world scenarios, demonstrating accuracy comparable to conventional manual digitization. The algorithm has been developed as an open-source R package and as a Shiny application and is available on GitHub: https://github.com/Pechli-Lab/SurvdigitizeR and https://pechlilab.shinyapps.io/SurvdigitizeR/ .

Construction of a clinical prediction model for complicated appendicitis based on machine learning techniques.

Acute appendicitis is a typical surgical emergency worldwide and one of the common causes of surgical acute abdomen in the elderly. Accurately diagnosing and differentiating acute appendicitis can assist clinicians in formulating a scientific and reasonable treatment plan and providing high-quality medical services for the elderly. In this study, we validated and analyzed the different performances of various machine learning models based on the analysis of clinical data, so as to construct a simple, fast, and accurate estimation method for the diagnosis of early acute appendicitis. The dataset of this paper was obtained from the medical data of elderly patients with acute appendicitis attending the First Affiliated Hospital of Anhui University of Chinese Medicine from January 2012 to January 2022, including 196 males (60.87%) and 126 females (39.13%), including 103 (31.99%) patients with complicated appendicitis and 219 (68.01%) patients with uncomplicated appendicitis. By comparing and analyzing the prediction results of the models implemented by nine different machine learning techniques (LR, CART, RF, SVM, Bayes, KNN, NN, FDA, and GBM), we found that the GBM algorithm gave the optimal results and that sensitivity, specificity, PPV, NPV, precision, recall, F1 and brier are 0.9167, 0.9739, 0.9429, 0.9613, 0.9429, 0.9167, 0.9296, and 0.05649, respectively. The GBM model prediction results are interpreted using the SHAP technology framework. Calibration and Decision curve analysis also show that the machine learning model proposed in this paper has some clinical and economic benefits. Finally, we developed the Shiny application for complicated appendicitis diagnosis to assist clinicians in quickly and effectively recognizing patients with complicated appendicitis (CA) and uncomplicated appendicitis (UA), and to formulate a more reasonable and scientific clinical plan for acute appendicitis patient population promptly.

"ClusterApp": A Shiny R application to guide cluster studies based on GPS data.

The rapid evolution of GPS devices, and therefore, collection of GPS data can be used to investigate a wide variety of topics in wildlife research. The combination of remotely collected GPS data with on-the-ground field investigations is a powerful tool for exploring behavioral ecology. "GPS cluster studies" are aimed at pinpointing and investigating identified clusters in the field. Activity clusters can be based on various parameters (e.g., distance between GPS locations and the number of locations needed to establish a cluster), which are closely related to the set research questions. Variation in methods across years within the same study may result in data collection biases. Therefore, a streamlined method to parametrize, generate interactive maps, and extract activity cluster data using a predefined approach will limit biases, and make field work and data management straightforward for field technicians. We developed the "ClusterApp" Shiny application in the R software to facilitate a step-by-step guide to execute cluster analyses and data management of cluster studies on any species using GPS data. We illustrate the use of the "ClusterApp" with two location datasets constructed by data collected on brown bears (Ursus arctos) and gray wolves (Canis lupus).

PROpwr: a Shiny R application to analyze patient-reported outcomes data and estimate power.

Patient Reported Outcomes (PROs) are widely used in quality of life (QOL) studies, health outcomes research, and clinical trials. The importance of PRO has been advocated by health authorities. We propose this R shiny web application, PROpwr, that estimates power for two-arm clinical trials with PRO measures as endpoints using Item Response Theory (GRM: Graded Response Model) and simulations. PROpwr also supports the analysis of PRO data for convenience of estimating the effect size. There are seven function tabs in PROpwr: Frequentist Analysis, Bayesian Analysis, GRM power, T-test Power Given Sample Size, T-test Sample Size Given Power, Download, and References. PROpwr is user-friendly with point-and-click functions. PROpwr can assist researchers to analyze and calculate power and sample size for PRO endpoints in clinical trials without prior programming knowledge.

The Usefulness of Posterior Shiny Corner Lesions in the Early Diagnosis of Medial Meniscus Posterior Root Tears.

INTRODUCTION:  Posterior shiny corner lesions (PSCLs) have been reported to be useful for the early diagnosis of medial meniscus posterior root tears (MMPRTs) in surgical patients. However, the usefulness of PSCLs in outpatients, particularly regarding the optimal timing of magnetic resonance imaging (MRI) examinations after injury, remains unknown. We hypothesized that PSCLs would normally be observed in patients with MMPRTs within one month of injury. MATERIALS AND METHODS:  This study included 144 patients with knee pain who visited our hospital between January 2021 and May 2023. MRI findings within and after one month were examined. Fisher's exact test was performed for PSCLs, cleft signs, ghost signs, radial tear signs, bone cysts, and medial meniscus extrusion (MME), which are findings used for the diagnosis of MMPRTs. Time-dependent receiver operating characteristic (ROC) curve analysis was performed for each MRI finding. A binomial logistic regression analysis was performed for age, sex, PSCL, ghost sign, and MME. RESULTS: PSCLs were observed on 82.6% of the MRI scans within one month, but the positivity rate decreased after one month. After one month, a high percentage of patients had cleft signs and ghost signs. The results of a time-dependent ROC curve analysis showed that the PSCL had better diagnostic ability than the cleft sign, ghost sign, radial tear sign, and MME at a relatively early stage. Additionally, the area under the curve (AUC) of PSCL peaks around 35 days and then declines, reaching 0.8 or less around 40 days. On the other hand, the AUC of the cleft sign and ghost sign began to increase around 30 days after injury, and it exceeded 0.8 after approximately 100 days. The results of the binomial logistic regression analysis revealed significant PSCLs and ghost signs. Independent associations between the PSCL, or ghost sign, and the MMPRT were demonstrated. CONCLUSION:  This study suggests that PSCLs have a superior diagnostic capability for MMPRT during the early stages of injury compared with other MRI findings in outpatients. In particular, PSCLs have a high positivity rate within one month after injury and a high diagnostic capacity up to 40 days after injury.

PCAS: An Integrated Tool for Multi-Dimensional Cancer Research Utilizing Clinical Proteomic Tumor Analysis Consortium Data.

Proteomics offers a robust method for quantifying proteins and elucidating their roles in cellular functions, surpassing the insights provided by transcriptomics. The Clinical Proteomic Tumor Analysis Consortium database, enriched with comprehensive cancer proteomics data including phosphorylation and ubiquitination profiles, alongside transcriptomics data from the Genomic Data Commons, allow for integrative molecular studies of cancer. The ProteoCancer Analysis Suite (PCAS), our newly developed R package and Shinyapp, leverages these resources to facilitate in-depth analyses of proteomics, phosphoproteomics, and transcriptomics, enhancing our understanding of the tumor microenvironment through features like immune infiltration and drug sensitivity analysis. This tool aids in identifying critical signaling pathways and therapeutic targets, particularly through its detailed phosphoproteomic analysis. To demonstrate the functionality of the PCAS, we conducted an analysis of GAPDH across multiple cancer types, revealing a significant upregulation of protein levels, which is consistent with its important biological and clinical significance in tumors, as indicated in our prior research. Further experiments were used to validate the findings performed using the tool. In conclusion, the PCAS is a powerful and valuable tool for conducting comprehensive proteomic analyses, significantly enhancing our ability to uncover oncogenic mechanisms and identify potential therapeutic targets in cancer research.

K-Track-Covid: interactive web-based dashboard for analyzing geographical and temporal spread of COVID-19 in South Korea.

The COVID-19 pandemic has necessitated the development of robust tools for tracking and modeling the spread of the virus. We present 'K-Track-Covid,' an interactive web-based dashboard developed using the R Shiny framework, to offer users an intuitive dashboard for analyzing the geographical and temporal spread of COVID-19 in South Korea. Our dashboard employs dynamic user interface elements, employs validated epidemiological models, and integrates regional data to offer tailored visual displays. The dashboard allows users to customize their data views by selecting specific time frames, geographic regions, and demographic groups. This customization enables the generation of charts and statistical summaries pertinent to both daily fluctuations and cumulative counts of COVID-19 cases, as well as mortality statistics. Additionally, the dashboard offers a simulation model based on mathematical models, enabling users to make predictions under various parameter settings. The dashboard is designed to assist researchers, policymakers, and the public in understanding the spread and impact of COVID-19, thereby facilitating informed decision-making. All data and resources related to this study are publicly available to ensure transparency and facilitate further research.

CPADS: a web tool for comprehensive pancancer analysis of drug sensitivity.

Drug therapy is vital in cancer treatment. Accurate analysis of drug sensitivity for specific cancers can guide healthcare professionals in prescribing drugs, leading to improved patient survival and quality of life. However, there is a lack of web-based tools that offer comprehensive visualization and analysis of pancancer drug sensitivity. We gathered cancer drug sensitivity data from publicly available databases (GEO, TCGA and GDSC) and developed a web tool called Comprehensive Pancancer Analysis of Drug Sensitivity (CPADS) using Shiny. CPADS currently includes transcriptomic data from over 29 000 samples, encompassing 44 types of cancer, 288 drugs and more than 9000 gene perturbations. It allows easy execution of various analyses related to cancer drug sensitivity. With its large sample size and diverse drug range, CPADS offers a range of analysis methods, such as differential gene expression, gene correlation, pathway analysis, drug analysis and gene perturbation analysis. Additionally, it provides several visualization approaches. CPADS significantly aids physicians and researchers in exploring primary and secondary drug resistance at both gene and pathway levels. The integration of drug resistance and gene perturbation data also presents novel perspectives for identifying pivotal genes influencing drug resistance. Access CPADS at https://smuonco.shinyapps.io/CPADS/ or https://robinl-lab.com/CPADS.

Corrigendum: Identifying predictors of clinical outcomes using the projection-predictive feature selection-a proof of concept on the example of Crohn's disease.

[This corrects the article DOI: 10.3389/fped.2023.1170563.].

The Health Equity Explorer: An open-source resource for distributed health equity visualization and research across common data models.

Introduction: There is an urgent need to address pervasive inequities in health and healthcare in the USA. Many areas of health inequity are well known, but there remain important unexplored areas, and for many populations in the USA, accessing data to visualize and monitor health equity is difficult. Methods: We describe the development and evaluation of an open-source, R-Shiny application, the "Health Equity Explorer (H2E)," designed to enable users to explore health equity data in a way that can be easily shared within and across common data models (CDMs). Results: We have developed a novel, scalable informatics tool to explore a wide variety of drivers of health, including patient-reported Social Determinants of Health (SDoH), using data in an OMOP CDM research data repository in a way that can be easily shared. We describe our development process, data schema, potential use cases, and pilot data for 705,686 people who attended our health system at least once since 2016. For this group, 996,382 unique observations for questions related to food and housing security were available for 324,630 patients (at least one answer for all 46% of patients) with 65,152 (20.1% of patients with at least one visit and answer) reporting food or housing insecurity at least once. Conclusions: H2E can be used to support dynamic and interactive explorations that include rich social and environmental data. The tool can support multiple CDMs and has the potential to support distributed health equity research and intervention on a national scale.

Stacked probability plots of the extended illness-death model using constant transition hazards - an easy to use shiny app.

BACKGROUND: Extended illness-death models (a specific class of multistate models) are a useful tool to analyse situations like hospital-acquired infections, ventilation-associated pneumonia, and transfers between hospitals. The main components of these models are hazard rates and transition probabilities. Calculation of different measures and their interpretation can be challenging due to their complexity. METHODS: By assuming time-constant hazards, the complexity of these models becomes manageable and closed mathematical forms for transition probabilities can be derived. Using these forms, we created a tool in R to visualize transition probabilities via stacked probability plots. RESULTS: In this article, we present this tool and give some insights into its theoretical background. Using published examples, we give guidelines on how this tool can be used. Our goal is to provide an instrument that helps obtain a deeper understanding of a complex multistate setting. CONCLUSION: While multistate models (in particular extended illness-death models), can be highly complex, this tool can be used in studies to both understand assumptions, which have been made during planning and as a first step in analysing complex data structures. An online version of this tool can be found at https://eidm.imbi.uni-freiburg.de/ .

Development of MetaXplore: An Interactive Tool for Targeted Metagenomic Analysis.

Over the last decades, the analysis of complex microbial communities by high-throughput sequencing of marker gene amplicons has become routine work for many research groups. However, the main challenges faced by scientists who want to make use of the generated sequencing datasets are the lack of expertise to select a suitable pipeline and the need for bioinformatics or programming skills to apply it. Here, we present MetaXplore, an interactive, user-friendly platform that enables the discovery and visualization of amplicon sequencing data. Currently, it provides a set of well-documented choices for downstream analysis, including alpha and beta diversity analysis, taxonomic composition, differential abundance analysis, identification of the core microbiome within a population, and biomarker analysis. These features are presented in a user-friendly format that facilitates easy customization and the generation of publication-quality graphics. MetaXplore is implemented entirely in the R language using the Shiny framework. It can be easily used locally on any system with R installed, including Windows, Mac OS, and most Linux distributions, or remotely via a web server without bioinformatic expertise. It can also be used as a framework for advanced users who can modify and expand the tool.

CITEViz: interactively classify cell populations in CITE-Seq via a flow cytometry-like gating workflow using R-Shiny.

BACKGROUND: The rapid advancement of new genomic sequencing technology has enabled the development of multi-omic single-cell sequencing assays. These assays profile multiple modalities in the same cell and can often yield new insights not revealed with a single modality. For example, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-Seq) simultaneously profiles the RNA transcriptome and the surface protein expression. The surface protein markers in CITE-Seq can be used to identify cell populations similar to the iterative filtration process in flow cytometry, also called "gating", and is an essential step for downstream analyses and data interpretation. While several packages allow users to interactively gate cells, they often do not process multi-omic sequencing datasets and may require writing redundant code to specify gate boundaries. To streamline the gating process, we developed CITEViz which allows users to interactively gate cells in Seurat-processed CITE-Seq data. CITEViz can also visualize basic quality control (QC) metrics allowing for a rapid and holistic evaluation of CITE-Seq data. RESULTS: We applied CITEViz to a peripheral blood mononuclear cell CITE-Seq dataset and gated for several major blood cell populations (CD14 monocytes, CD4 T cells, CD8 T cells, NK cells, B cells, and platelets) using canonical surface protein markers. The visualization features of CITEViz were used to investigate cellular heterogeneity in CD14 and CD16-expressing monocytes and to detect differential numbers of detected antibodies per patient donor. These results highlight the utility of CITEViz to enable the robust classification of single cell populations. CONCLUSIONS: CITEViz is an R-Shiny app that standardizes the gating workflow in CITE-Seq data for efficient classification of cell populations. Its secondary function is to generate basic feature plots and QC figures specific to multi-omic data. The user interface and internal workflow of CITEViz uniquely work together to produce an organized workflow and sensible data structures for easy data retrieval. This package leverages the strengths of biologists and computational scientists to assess and analyze multi-omic single-cell datasets. In conclusion, CITEViz streamlines the flow cytometry gating workflow in CITE-Seq data to help facilitate novel hypothesis generation.

Easy-Amanida: An R Shiny application for the meta-analysis of aggregate results in clinical metabolomics using Amanida and Webchem.

Meta-analysis is a useful tool in clinical research, as it combines the results of multiple clinical studies to improve precision when answering a particular scientific question. While there has been a substantial increase in publications using meta-analysis in various clinical research topics, the number of published meta-analyses in metabolomics is significantly lower compared to other omics disciplines. Metabolomics is the study of small chemical compounds in living organisms, which provides important insights into an organism's phenotype. However, the wide variety of compounds and the different experimental methods used in metabolomics make it challenging to perform a thorough meta-analysis. Additionally, there is a lack of consensus on reporting statistical estimates, and the high number of compound naming synonyms further complicates the process. Easy-Amanida is a new tool that combines two R packages, "amanida" and "webchem", to enable meta-analysis of aggregate statistical data, like p-value and fold-change, while ensuring the compounds naming harmonization. The Easy-Amanida app is implemented in Shiny, an R package add-on for interactive web apps, and provides a workflow to optimize the naming combination. This article describes all the steps to perform the meta-analysis using Easy-Amanida, including an illustrative example for interpreting the results. The use of aggregate statistics metrics extends the use of Easy-Amanida beyond the metabolomics field.

Diving into CDC pregnancy data in the United States: longitudinal study and interactive application.

Objective: Preterm birth (PTB) is a major determinant of neonatal mortality, morbidity, and childhood disability. In this article, we present a longitudinal analysis of the risk factors associated with PTB and how they have varied over the years: starting from 1968 when the CDC first started, reporting the natality data, up until 2021. Along with this article, we are also releasing an RShiny web application that will allow for easy consumption of this voluminous dataset by the research community. Further, we hope this tool can aid clinicians in the understanding and prevention of PTB. Materials and Methods: This study used the CDC Natality data from 1968 to 2021 to analyze trends in PTB outcomes across the lens of various features, including race, maternal age, education, and interval length between pregnancies. Our interactive RShiny web application, CDC NatView, allows users to explore interactions between maternal risk factors and maternal morbidity conditions and the aforementioned features. Results: Our study demonstrates how CDC data can be leveraged to conduct a longitudinal analysis of natality trends in the United States. Our key findings reveal an upward trend in late PTBs, which is concerning. Moreover, a significant disparity exists between African American and White populations in terms of PTB. These disparities persist in other areas, such as education, body-mass index, and access to prenatal care later in pregnancy. Discussion: Another notable finding is the increase in maternal age over time. Additionally, we confirm that short interpregnancy intervals (IPIs) are a risk factor for PTBs. To facilitate the exploration of pregnancy risk factors, infections, and maternal morbidity, we developed an open-source RShiny tool called CDC NatView. This software offers a user-friendly interface to interact with and visualize the CDC natality data, which constitutes an invaluable resource. Conclusion: In conclusion, our study has shed light on the rise of late PTBs and the persistent disparities in PTB rates between African American and White populations in the US. The increase in maternal age and the confirmation of a short IPI as a risk factor for PTB are noteworthy findings. Our open-source tool, CDC NatView, can be a valuable resource for further exploration of the CDC natality data to enhance our understanding of pregnancy risk factors and the interaction of PTB outcomes and maternal morbidities.

Laboratory Automated Interrogation of Data: an interactive web application for visualization of multilevel data from biological experiments.

A key step in understanding the results of biological experiments is visualization of the data. Many laboratory experiments contain a range of measurements that exist within a hierarchy of interdependence. An automated and facile way to visualize and interrogate such multilevel data, across many experimental variables, would (i) lead to improved understanding of the results, (ii) help to avoid misleading interpretation of statistics and (iii) easily identify outliers and sources of batch and confounding effects. While many excellent graphing solutions already exist, they are often geared towards the production of publication-ready plots and the analysis of a single variable at a time, require programming expertise or are unnecessarily complex for the task at hand. Here, we present Laboratory Automated Interrogation of Data (LAB-AID), an interactive tool specifically designed to automatically visualize and query hierarchical data resulting from biological experiments.