Informatics Tools

Error message

  • Deprecated function: Optional parameter $checkbox declared before required parameter $input is implicitly treated as a required parameter in include_once() (line 1442 of /local/drupal/itcr/includes/bootstrap.inc).
  • Warning: Undefined property: stdClass::$field_info_tools_link_6i in eval() (line 23 of /local/drupal/itcr/sites/default/modules/views_php/plugins/views/views_php_handler_field.inc(235) : eval()'d code).
  • Deprecated function: Optional parameter $key declared before required parameter $is_multi is implicitly treated as a required parameter in require_once() (line 342 of /local/drupal/itcr/includes/module.inc).
  • Deprecated function: Optional parameter $route declared before required parameter $is_multi is implicitly treated as a required parameter in require_once() (line 342 of /local/drupal/itcr/includes/module.inc).
  • Deprecated function: Return type of crumbs_PluginSystem_PluginMethodIterator::current() should either be compatible with Iterator::current(): mixed, or the #[\ReturnTypeWillChange] attribute should be used to temporarily suppress the notice in require_once() (line 4 of /local/drupal/itcr/sites/all/modules/crumbs/lib/PluginSystem/PluginMethodIterator.php).
  • Deprecated function: Return type of crumbs_PluginSystem_PluginMethodIterator::next() should either be compatible with Iterator::next(): void, or the #[\ReturnTypeWillChange] attribute should be used to temporarily suppress the notice in require_once() (line 4 of /local/drupal/itcr/sites/all/modules/crumbs/lib/PluginSystem/PluginMethodIterator.php).
  • Deprecated function: Return type of crumbs_PluginSystem_PluginMethodIterator::key() should either be compatible with Iterator::key(): mixed, or the #[\ReturnTypeWillChange] attribute should be used to temporarily suppress the notice in require_once() (line 4 of /local/drupal/itcr/sites/all/modules/crumbs/lib/PluginSystem/PluginMethodIterator.php).
  • Deprecated function: Return type of crumbs_PluginSystem_PluginMethodIterator::valid() should either be compatible with Iterator::valid(): bool, or the #[\ReturnTypeWillChange] attribute should be used to temporarily suppress the notice in require_once() (line 4 of /local/drupal/itcr/sites/all/modules/crumbs/lib/PluginSystem/PluginMethodIterator.php).
  • Deprecated function: Return type of crumbs_PluginSystem_PluginMethodIterator::rewind() should either be compatible with Iterator::rewind(): void, or the #[\ReturnTypeWillChange] attribute should be used to temporarily suppress the notice in require_once() (line 4 of /local/drupal/itcr/sites/all/modules/crumbs/lib/PluginSystem/PluginMethodIterator.php).
×

The ITCR Program funds informatics tools that support data across the cancer research continuum. All of the tools are free for use by academic and non-profit researchers. Access to tools, code repositories and introductory videos is available through the links in the table below.

Searching and Filtering Guidelines

Tool Name Tool Description Date Added
Network Analysis of Immune Repertoire (NAIR)
Immuno-oncology

NAIR, Network Analysis of Immune Repertoire, is an R package using network analysis and machine learning to explore immune receptor (TCR/BCR) sequences. Users can search and visualize disease-associated/shared sequence clusters and perform downstream analysis. It supports amino acid and nucleotide sequences, multiple distance metrics, and bulk and single-cell data.

09/19/2023
Averon Notebook
Proteomics

Averon Notebook provides a computational environment to identify new therapeutically actionable mechanisms of oncogenic signaling enabled by mutant-directed protein-protein interactions to inform target discovery in cancer.

09/16/2023
spatialGE web application
Transcriptomics

spatialGE is a user friendly, point-and-click, web application that facilitates spatial transcriptomics data analysis. This application contains a collection of analytical methods for visualization and statistical analysis of the tissue microenvironment. Users can create accounts to manage their data and projects, as well as generate figures and tables to report results.

09/10/2023
spatialGE R package
Transcriptomics

spatialGE R package is an analytical suite for the visualization and spatial statistics analysis of spatially-resolved transcriptomics data. The spatialGE R package features a data object to store data and results from multiple tissue sections, as well as associated methods to detect spatial patterns in the expression of individual genes and gene sets. 

09/10/2023
mCodeGPT
Medical Informatics

This Python package harnesses the power of large language models like GPT-4 to automatically extract entities from raw text associated with a given cancer ontologies and Knowledge Bases. Input research text and mCodeGPT will output structured data in tabular format. 

09/10/2023
Overture
Analysis Platform

Overture is a collection of modular, open-source software components designed to make the management of big-data genomic projects both easy and more cost effective. The Overture system promotes FAIR data sharing of genomic datasets by overcoming the major obstacles in storing, managing, exploring, and distributing massive genome-scale datasets.

08/29/2023
OpenChallenges
Analysis Platform

OpenChallenges.io is a centralized hub for biomedical challenges that empowers participants with the most up-to-date information about relevant challenges, while providing organizers with standardized challenge event templates and intelligence.

08/29/2023
Lancet2
Genomics

Next generation of Lancet, a local-assembly based somatic variant caller for short read sequencing data, with improved runtime and genotyping performance.

08/23/2023
ARCHS4
Transcriptomics

ARCHS4 provides gene and transcript counts uniformly processed from all the human and mouse RNA-seq samples from GEO.

08/11/2023
International Skin Imaging Collaboration Archive
Medical Informatics, Pathology Imaging

The ISIC Archive is a web-based platform to support the sharing, management and analysis of dermatology imaging data. We currently host over 70,000 public images. The ITCR funding is to support improved dataset curation for various educational and machine learning purposes as well as integration of reflectance confocal microscopy data.

08/04/2023
Lisa: Epigenetic Landscape In Silico deletion Analysis
Epigenetics, Transcriptomics

Lisa is a web-based tool and Python software package for predicting transcriptional regulators of differentially expressed gene sets. Lisa combines histone modification ChIP-seq and chromatin accessibility profiles to identify cis-regulatory regions, and uses transcription factor ChIP-seq to determine relevant regulatory transcription factors.

07/26/2023
JBrowse 2
Visualization

JBrowse 2 is the new version of the JBrowse genome browser, available as a desktop application, a web application, and embeddable web components. It expands on JBrowse 1 by adding support for showing multiple visualizations, including synteny, circular, breakpoint detail, and tabular views. It also has integrations with Jupyter notebooks and R, and a growing library of plugins.

07/26/2023
MIRA: Multimodal models for Integrated Regulatory Analysis
Epigenetics, Transcriptomics

MIRA is a Python software package for analyzing single cell RNA-seq, ATAC-seq and multimodal data. MIRA includes effective batch correction methods for both modalities and infers gene regulatory mechanisms and regulatory transcription factors through integrative analyses of joint RNA and chromatin accessibility modalities.

07/26/2023
Integrated Methods for Predicting Enhancer Targets (IM-PET)
Epigenetics, Genomics, Transcriptomics

IM-PET is an open source software tool for identifying target genes of transcriptional enhancers. It uses four statistical features derived from transcriptomic, genomic, and epigenomic data. IM-PET is also available as a Docker container.

07/25/2023
ecSeg
Genomics

This repository is the official version of ecSeg, a tool used to quantify ecDNA in DAPI-stained images. It also has an extension to analyze FISH probes.

12/31/2021
FaNDOM
Genomics

FaNDOM is a fast and open source method for aligning Bionano Saphyr optical map molecules and contigs to a reference, with the goal of identifying structural variation in genomes. FaNDOM utilizes a seed-based filter to speed up the searches. FaNDOM is implemented in C++ and supports multithreading.

12/13/2021
AmpliconReconstructor (AR)
Genomics

Reconstructs complex variation and disambiguates Amplicon Architect based reconstructions using BioNano optical mapping data and an NGS-derived breakpoint graph.

12/13/2021
AmpliconArchitect (AA)
Genomics

AmpliconArchitect (AA) is a tool which can reconstruct the structure of focally amplified regions in a cancer sample using whole genome sequence short paired-end data. A full description of the methods and detailed characterization of copy number amplifications and ecDNA in cancer can be found in the following manuscript.

12/13/2021
KiNet
Pathology Imaging

KiNet is an open-source software tool for automated Ki67 labeling index assessment in digital pathology images.

12/10/2021
PRECISION.seq
Transcriptomics

PRECISION.seq enables an objective and systemic evaluation of depth normalization methods for microRNA sequencing, in the context of differential expression analysis, using realistically distributed and robustly benchmarked data. Users can assess their chosen methods and compare their performance to nine methods already implemented in the package.

12/02/2021

Pages