Software Tools

Pecar Lab

EC Atlas

EC Atlas is a resource containing the single cell transcriptome atlas of murine normal endothelial cells.

The endothelial cell atlas database is a freely accessible database that facilitates the exploration and exposition of the data and analyses of the corresponding accompanying paper (PubMed) in a user-friendly way.

Click here to access the database.

Pecar Lab

EndoDB

The endothelial cell database (EndoDB) is a freely accessible added-value database that facilitates bench scientists to unlock the untapped potential of publicly available (single cell) transcriptomics data (Pubmed).

Click here to access the database.

Pecar Lab

Lung tumor ECTax

The lung tumor endothelial cell taxonomy database is a freely accessible database that facilitates the exploration and exposition of the data and analyses of the corresponding accompanying paper (PubMed) in a user-friendly way.

Click here to access the database.

Pecar Lab

Murine ECTax

Murine ECTax is a resource containing the single cell transcriptome  taxonomy of murine choroidal neovascularaziation endothelial cells.

The murine choroidal neovascularization endothelial cell taxonomy database is a freely accessible database that facilitates the exploration and exposition of the data and analyses of the corresponding accompanying paper in a user-friendly way.

Click here to access the database.

Pecar Lab

REC dehydration

The renal endothelial cell taxonomy database is a freely accessible database that facilitates the exploration and exposition of the data and analyses of the corresponding accompanying paper (PubMed) in a user-friendly way.

Click here to access the database.

Sscylce

scCycle

scCycle is a database of cell cycle associated genes in proliferating endothelial cells during pathological angiogenesis.

Click here to access the database

Pecar Lab

BIOMEX

Biomex is a software to facilitate the analysis of (single cell) omics data

Pecar Lab

AI4TargetDiscovery-v1.0

AI4TargetDicovery-v1.0 is an Artificial Intelligence/Machine Learning framework developed for identification and prioritization of target genes based on PU learning (Learning from positive and unlabeled data). The current model is designed to predict angiogenic genes by considering genes with unknown angiogenic function as an unlabeled set (U) rather than a negative set (N). The framework employs a concatenated matrix of gene-level features (derived from bulk RNA sequencing datasets) together manually curated causal angiogenic genes as positive training instances.

The tool will be made accessible upon publication

Pecar Lab

SCMYSTERYDENTIFIER-V2.0

scMysterYdentifier-v2.0 is a neural network model-based deep learning (DL) classifier integrating scRNA-sequencing data and an in-house highly curated list of training genes, to predict immunosuppressive genes among to date uncharacterized (“mystery genes”) or poorly characterized genes expressed in endothelial cells. Briefly, these training genes have a known immunosuppressive function, and based on a ‘guilt-by-association’ strategy, scMysterYdentifier-v2.0 predicts a list of candidate genes with an immunosuppressive function, including both well-characterized genes and mystery genes. Subsequently, the tool identifies mystery genes within this list by robustly assessing, via text mining, whether a gene has an annotated function that is extensively or minimally studied in ECs.

The tool will be made accessible upon publication.

Pecar Lab

BfBio-v1.0

Under development.

Brain-for-BioTech (BfBio) is an AI/ML-based gene discovery tools for predicting immunomodulatory functions for poorly characterized / uncharacterized genes, expressed in endothelial cells.

Pecar Lab

DL4CPath

DL4Cpath is an AI tool to automate histological quantification of tumor area on whole slide images (WSI). It allows an accurate segmentation of tumor regions and assessment of tumor burden comparable to the values obtained by manual delineation by an expert reader. The tool not only enhances the speed and accuracy of the WSI analysis but also contributes to standardizing the analysis across multiple samples, ensuring increased consistency. The model is generic and can be applied to WSIs with different tissue staining including immunofluorescence.

The tool will be made accessible upon publication.

Pecar Lab

Mega human single-EC Atlas

Under development.

This atlas will combine all available single cell RNA-sequencing studies on human endothelial cells (ECs) in health and disease. The atlas will facilitate the discovery of novel differentially expressed genes in tumor ECs versus ECs in the corresponding healthy tissue.