Tools   Select Another Resource Report Type

https://github.com/nanoporetech/pod5-file-format

File format for storing nanopore DNA data in an easily accessible way. High performance file format for nanopore reads.

Proper citation: pod5 (RRID:SCR_028166) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/release/bioc/html/scuttle.html

Software R package provides some legacy utility functions for performing single-cell analyses. Most of these functions are deprecated in favor of newer, more performant alternatives. We just keep this package around for back-compatibility and to point to the replacement functions.

Proper citation: scuttle (RRID:SCR_028419) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages/release/data/experiment/html/scRNAseq.html

Software R package for collection of public scRNA-seq datasets, provided as SingleCellExperiment objects with cell- and gene-level metadata.

Proper citation: scRNAseq (RRID:SCR_028417) Copy   

•   Source: SciCrunch Registry

https://www.bioconductor.org/packages//release/data/experiment/html/TabulaMurisData.html

Software R package for access to processed 10x (droplet) and SmartSeq2 (on FACS-sorted cells) single-cell RNA-seq data from the Tabula Muris consortium.

Proper citation: TabulaMurisData (RRID:SCR_028418) Copy   

•   Source: SciCrunch Registry

https://doi.org/10.32614/CRAN.package.pairwiseCI

Software R package provides wrapper functions to compute parametric, nonparametric, and bootstrap confidence intervals (CIs) for comparing two samples, specifically designed for all-pairs or many-to-one comparisons. It enables, but does not enforce, adjustments for multiple testing.

Proper citation: pairwiseCI (RRID:SCR_028345) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/lf_patches/

Software MATLAB toolbox for the automatic segmentation of the hippocampus in brain MRI images. It implements a novel patch-based label fusion method that cooperates with a non-rigid registration-based label fusion approach. Used to automatically and accurately segment the hippocampus in MRI scans by combining two techniques.

Proper citation: Combining a patch-based approach with a non-rigid registration-based label fusion method for the hippocampal segmentation (RRID:SCR_028349) Copy   

•   Source: SciCrunch Registry

https://mdv.ndm.ox.ac.uk/docs/documentation/using-chatmdv

Software tool as natural language interface integrated with MDV that allows users to generate high-quality interactive visualisations through natural language commands. ChatMDV employs a retrieval-augmented generation (RAG) pipeline combined with large language models (LLMs) to translate user queries into reproducible Python code and interactive output. Module to add chatbot functionality to query Multi-Dimensional Viewer projects.

Proper citation: ChatMDV (RRID:SCR_028342) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/readr/index.html

Software R package read flat files (csv, tsv, fwf) into R. Used to read rectangular data like 'csv', 'tsv', and 'fwf'. Designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.

Proper citation: readr (RRID:SCR_028451) Copy   

•   Source: SciCrunch Registry

https://lume.tv/PANGEA/

Spacial neuron gene expression atlas. Interactive, server-free web application and spatial transcriptomics database designed to help researchers map and analyze gene expression within the brain. Mouse whole brain spatial transcriptomic atlas.

Proper citation: PANGEA (RRID:SCR_028559) Copy   

•   Source: SciCrunch Registry

https://www.embl-hamburg.de/biosaxs/dammif.html

Software tool for rapidly determining the low-resolution three-dimensional shape of biological macromolecules in solution using Small-Angle X-ray Scattering (SAXS) data. Used for rapid ab-initio shape determination in small-angle scattering.

Proper citation: DAMMIF (RRID:SCR_028444) Copy   

•   Source: SciCrunch Registry

https://bioconductor.posit.co/packages/3.20/data/annotation/html/IlluminaHumanMethylationEPICv2anno.20a1.hg38.html

Software R annotation package for Illumina's EPIC v2.0 methylation arrays. The version 2 covers more than 935K CpG sites in the human genome hg38. It is an update of the original EPIC v1.0 array (i.e., the 850K methylation array).

Proper citation: IlluminaHumanMethylationEPICv2anno (RRID:SCR_028569) Copy   

•   Source: SciCrunch Registry

https://gatk.broadinstitute.org/hc/en-us/articles/360036350452-VariantFiltration

Software command-line tool designed for hard-filtering variant callsets (VCF files) by applying user-defined criteria to annotate, rather than remove, low-quality variants. It marks fails in the FILTER field (e.g., using JEXL expressions to filter by DP, QD, or FS), making it essential for filtering small datasets, non-model organisms, or whenever Variant Quality Score Recalibration (VQSR) is not feasible

Proper citation: GATK VariantFiltration (RRID:SCR_028441) Copy   

•   Source: SciCrunch Registry

https://genome.ucsc.edu/goldenpath/help/bigWig.html

Command-line utility provided by the UCSC Genome Browser to convert text-based bedGraph files into indexed binary bigWig files. It is specifically used in bioinformatics to transform dense, continuous genome coverage data into a format that enables fast visualization and remote viewing in genome browsers like IGV or the UCSC Genome Browser.

Proper citation: bedGraphToBigWig (RRID:SCR_028439) Copy   

•   Source: SciCrunch Registry

https://www.scienceverse.org/metacheck/

Software R package to audit research outputs for compliance with open science best practices. Evaluates adherence to standards such as pre-registration and data availability. Used for automated checks of research outputs for best practices.

Proper citation: MetaCheck (RRID:SCR_028666) Copy   

•   Source: SciCrunch Registry

https://mycompounddiscoverer.com/

Software platform by Thermo Fisher Scientific designed for identifying, comparing, and interpreting small molecules in complex biological, environmental, and forensic samples. It uses customizable workflow, known as nodes, to automate mass spectrometry data processing, spectral library searching, and statistical analysis.Compound Discoverer is integrated with SIRIUS (via a custom workflow node) to bridge the gap between high-resolution MS/MS data and confident molecular identification. While Thermo Scientific’s Compound Discoverer excels at library searching and statistical analysis, SIRIUS provides powerful in silico tools to accurately predict molecular formulas, chemical classes, and de novo structures. High-resolution mass spectrometry (HRMS) data analysis software for untargeted metabolomics, lipidomics, and contaminant screening. Utilizes modular workflows to extract features, match spectra against libraries like mzCloud, and confidently identify complex organic compounds.

Proper citation: Compound Discoverer (RRID:SCR_028693) Copy   

•   Source: SciCrunch Registry

https://stoeltingco.com/Neuroscience/ANY-maze-Video-Tracking-Software~9825?navigate_from_document=1135&navigated_from_object=3955

Automated platform used in behavioral neuroscience to track and analyze the movements and behaviors of lab animals, such as mice and rats. Standardizes experiments like the Elevated Plus Maze, Open Field, Barnes Maze, and Fear Conditioning. Tracks whole-body movement, distance traveled, freezing/immobility, and zone entries. Connects to external devices like food dispensers, shockers, and lasers to trigger automated responses based on the animal's actions.

Proper citation: Stoelting ANY-maze Video Tracking Software (RRID:SCR_028718) Copy   

•   Source: SciCrunch Registry

https://insitupy.readthedocs.io/en/latest/

Software Python package for analysis of single-cell spatial transcriptomics data. Used to read, visualize, and analyze the spatially resolved gene expression within one dataset but also across different datasets. Provides general structure for organizing multiple datasets and its corresponding metadata.

Proper citation: InSitupy (RRID:SCR_028769) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/package=ppcor

Software R Package to calculates partial and semi-partial (part) correlations along with p-value. Fast Calculation to Semi-partial Correlation Coefficients.

Proper citation: ppcor (RRID:SCR_028755) Copy   

•   Source: SciCrunch Registry

https://github.com/dmcable/spacexr

Software R package for learning cell types and cell type-specific differential expression in spatial transcriptomics data. Used for cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics.

Proper citation: spacexr (RRID:SCR_028764) Copy   

•   Source: SciCrunch Registry

http://toc.lbg.ac.at/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. The projected cluster includes the LBIs for Applied Cancer Research, Clinical Oncology and Photodynamic Therapy, Gynecology and Gynecologic Oncology, Stem Cell Transplantation and Surgical Oncology. The aim of the projected cluster Translational Oncology is the cooperative investigation of genetic and molecular biological characteristics of the tumor cells involved in minimal residual disease (MRD) in vitro and translation of the experimental and diagnostic results into the clinical practice involving therapeutic modalities with the newest generation of antitumoral drugs. Minimal residual disease is the designation for the occurrence of a low number of tumor cells remaining clinically undetected following curative therapy that give rise to tumor relapses. MRD is a central question in cancer therapy, since a major subpopulation of patients which underwent curative resection and therapy ultimately relapse and would have received more aggressive adjuvant therapy, provided that residual disease had been clearly proven. Otherwise low-risk patients would have not been treated aggressively in an adjuvant setting. MRD can be detected by methods in bone marrow or by extremely sensitive PCR (polymerase-chain-reaction)-based methods in peripheral blood. PCR-based methods allow for the characterization of tumor-specific gene expression in circulating tumor cells and thereby provide additional information in regard to malignity of cells and prognosis. The different participating institutions have extensive experience in patient care, organization of clinical studies and laboratory investigation. In particular, expert knowledge in stem cell transplantation and histological detection of MRD, multicentric clinical testing of new anticancer drugs, specialized treatment of various selected tumor entities such as neuroendocrine tumors, gene expression analysis of circulating tumor cells and tumor signatures, and in vitro characterization of chemosensitivity as well as tumor cell biology have been acquired at the individual LBIs in the past and are complementary to each other to be combined in a larger cluster structure. The detection of circulating tumor cells will be supported by ongoing EU (OVCAD OVarian CAncer Diagnosis) and GenAU projects aiming at identification of ovarian cancer cells in the blood. The assessment of methylated DNA sequences (suppressor genes) in peripheral blood as an indicator of MRD can be performed with the help of OncoLab Diagnostics GmbH. Cooperative action in this cluster, using a common tumor bank/clinical data collection and the combined clinical and experimental efforts are the base for the execution of the presented MRD project.

Proper citation: Ludwig Boltzmann Cluster Translationale Onkologie (RRID:SCR_000020) Copy   

•   Source: SciCrunch Registry