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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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lda Resource Report Resource Website |
lda (RRID:SCR_027850) | software resource, software application | Software application for topic modeling with latent Dirichlet allocation. | Topic modeling, latent Dirichlet allocation, Gibbs sampling, | Free, Available for download, Freely available | SCR_027850 | 2026-08-12 10:53:51 | 0 | |||||||||||
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Tracker Resource Report Resource Website 1+ mentions |
Tracker (RRID:SCR_027845) | software resource, software application | Software video analysis and modeling tool developed within the Open Source Physics (OSP) Java framework. Allows frame-by-frame tracking of anatomical landmarks and articulated structures from video recordings, enabling the extraction of time-dependent kinematic variables such as displacement, velocity, and acceleration. Tracker is well suited for biomechanical analyses of articulated systems, as it supports joint-based rotations, reference-frame definition, and the export of quantitative motion data for further post-processing. | frame-by-frame tracking, anatomical landmarks and articulated structures, video recordings, extraction of time-dependent kinematic variables, | Free, Available for download, Freely available | SCR_027845 | Tracker Video Analysis and Modeling | 2026-08-12 10:53:51 | 6 | ||||||||||
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Developmental Human Brain Atlas Ontology (DHBA) Resource Report Resource Website 1+ mentions |
Developmental Human Brain Atlas Ontology (DHBA) (RRID:SCR_027940) | ontology, data or information resource, controlled vocabulary, source code, software resource | Machine-readable framework designed to standardize, organize, and annotate the anatomical structures, developmental stages, and spatial relationships of the human brain during development. It is primarily derived from the Allen Developing Human Brain Atlas (BrainSpan) to provide a structured, hierarchical taxonomy for researchers. Application ontology built by combining ontologised versions of the Allen Institute Developing Human Brain Atlas (DHBA) StructureGraph mapped to Uberon. | Allen Developing Human Brain Atlas, hierarchical taxonomy, standardize, organize, annotate, anatomical structures, developmental stages, spatial relationships, human brain, brain during development, Uberon, | is related to: Allen Human Brain Atlas: BrainSpan (Atlas of the Developing Brain) | Free, Available for download, Freely available | SCR_027940 | 2026-08-12 10:53:52 | 1 | ||||||||||
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BICAN Basal Ganglia Epigenome Explorer Resource Report Resource Website 1+ mentions |
BICAN Basal Ganglia Epigenome Explorer (RRID:SCR_027887) | data or information resource, portal | Portal that allows users to explore taxonomy-guided genome selections, visualize epigenetic assays, and analyze chromatin data across basal ganglia cell populations identified by the BRAIN Initiative Cell Atlas Network (BICAN) with an interactive research platform. The portal allows for investigation of several key epigenetic assays including associated with active enhancers and promoters, repressed genes, and constitutive heterochromatin. Used to analyze complex genomic and epigenomic data from the brain, helping identify specific cell types, understand gene regulation, and map disease-related molecular events, ultimately aiding in understanding neurological disorders like Alzheimer's, autism, and depression by revealing what goes wrong at the cellular level, leading to better gene therapies. | BICAN, explore taxonomy-guided genome selections, visualize epigenetic assays, analyze chromatin data, basal ganglia cell populations, basal ganglia epigenome, | is organization facet of: BRAIN Initiative Cell Atlas Network | Free, Freely available | SCR_027887 | 2026-08-12 10:54:04 | 1 | ||||||||||
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STICR Resource Report Resource Website 1+ mentions |
STICR (RRID:SCR_027856) | software resource, source code | Code to conduct combinatorial barcoding. scRNA-seq-compatible tracer for identifying clonal relationships. | scRNA-seq-compatible tracer, identifying clonal relationships, conduct combinatorial barcoding, | Free, Available for download, Freely available | SCR_027856 | 2026-08-12 10:53:51 | 1 | |||||||||||
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Spectroscopic Imaging, VIsualization, and Computing (SIVIC) Resource Report Resource Website 1+ mentions |
Spectroscopic Imaging, VIsualization, and Computing (SIVIC) (RRID:SCR_027875) | SIVIC | software resource, software application | Software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies. | DICOM MR Spectroscopy Workflows, data processing, data visualization, DICOM MR spectroscopy data, | NCI RO1 CA127612; NCI P01 CA11816; NIBIB P41EB013598 |
PMID:23970895 | Free, Available for download, Freely available | SCR_027875 | 2026-08-12 10:54:17 | 2 | ||||||||
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Purdue University Research Repository (PURR) Resource Report Resource Website |
Purdue University Research Repository (PURR) (RRID:SCR_027877) | PURR | service resource, data repository, storage service resource | Provides online, collaborative working space and data-sharing platform. Provides services with data management planning, boilerplate text for proposal, sample plans and individual consultation. Each dataset gets DOI. PURR publishes and archives digital datasets from researchers across campus and welcomes all kinds of open data from images and videos to spreadsheets and source code. | FAIR, DOI, open data, publishes and archives digital datasets, data-sharing platform, data management planning, boilerplate text for proposal, sample plans, consultation, | Restricted | SCR_027877 | 2026-08-12 10:54:04 | 0 | ||||||||||
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scrattch taxonomy Resource Report Resource Website 1+ mentions |
scrattch taxonomy (RRID:SCR_027910) | software toolkit, software resource, source code | Software R package from the Allen Institute designed to build, standardize, and analyze single-cell RNA-seq-based cell type taxonomies. It utilizes a structured Allen Institute schema (AIT) to organize cell annotations and metadata, enabling hierarchical, data-driven cell type classification | building cell type taxonomies, single cell RNA-seq data, Allen Institute (AIT) schema, | is related to: Allen Institute | Free, Available for download, Freely available | https://github.com/AllenInstitute/scrattch.taxonomy | SCR_027910 | 2026-08-12 10:54:04 | 1 | |||||||||
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DMRcate Resource Report Resource Website 1+ mentions |
DMRcate (RRID:SCR_028007) | software resource, software application | Software application for de novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulfite Sequencing (WGBS) and Illumina Infinium Array (450K and EPIC) data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes GRanges generation and plotting functions. | de novo identification and extraction, differentially methylated regions, human genome, | Free, Available for download, Freely available | SCR_028007 | 2026-08-12 10:54:18 | 2 | |||||||||||
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Poly Pipeline Resource Report Resource Website |
Poly Pipeline (RRID:SCR_027993) | software resource, software application | Software data analysis pipeline for spatial transcriptomics data tailored to polyploid organisms. | Spatial transcriptomics data, polyploid organisms, data analysis, | Free, Available for download, Freely available | https://zenodo.org/records/18655692 | SCR_027993 | 2026-08-12 10:53:53 | 0 | ||||||||||
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CIMA_BMI_paper Resource Report Resource Website |
CIMA_BMI_paper (RRID:SCR_028241) | software resource, source code | Source analysis and data processing code for article titled "Single-Cell Multi-Omics Insights into BMI-Mediated Immune-Related Disease Risk". | analysis and data processing code, Single-Cell Multi-Omics Insights, BMI-Mediated Immune-Related Disease Risk, | Free, Available for download, Freely available | SCR_028241 | 2026-08-12 10:53:56 | 0 | |||||||||||
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somalier Resource Report Resource Website |
somalier (RRID:SCR_028167) | software resource, software application | Software application for rapid relatedness estimation for cancer and germline studies using efficient genome sketches extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF. Used for rapid relatedness estimation for cancer and germline studies using efficient genome sketches. | rapid relatedness estimation, cancer and germline studies, efficient genome sketches, quality control, | NHGRI R41HG010126; NHGRI R01HG009141; NCI U24CA209999; NCI R37CA246183; NCI P30CA04014 |
PMID:32664994 | Free, Available for download, Freely available | SCR_028167 | Somalier | 2026-08-12 10:54:07 | 0 | ||||||||
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pod5 Resource Report Resource Website 10+ mentions |
pod5 (RRID:SCR_028166) | software resource, source code | File format for storing nanopore DNA data in an easily accessible way. High performance file format for nanopore reads. | File format, storing nanopore DNA data, DNA data, nanopore reads, | Free, Available for download, Freely available | SCR_028166 | POD5, pod5-file-format | 2026-08-12 10:54:19 | 11 | ||||||||||
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ChatMDV Resource Report Resource Website |
ChatMDV (RRID:SCR_028342) | software resource, software application | 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. | add chatbot functionality, query Multi-Dimensional Viewer projects, | DOI:10.1101/2025.08.26.671083 | Free, Available for download, Freely available | https://github.com/Taylor-CCB-Group/MDV | SCR_028342 | 2026-08-12 10:54:20 | 0 | |||||||||
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DAMMIF Resource Report Resource Website |
DAMMIF (RRID:SCR_028444) | software resource, software application | 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. | EMBL Hamburg BioSAXS group, determining low-resolution three-dimensional shape of biological macromolecules, macromolecules in solution, Small-Angle X-ray Scattering, | is related to: ATSAS | PMID:27630371 | Free, Available for download | SCR_028444 | Dummy Atom Model Fast | 2026-08-12 10:54:20 | 0 | ||||||||
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HemoGenix Resource Report Resource Website |
HemoGenix (RRID:SCR_028449) | commercial organization, service resource | Specialty contract research laboratory and biotechnology company that provides stem cell testing and in vitro toxicity screening, particularly for the blood-forming (hematopoietic) system. Provides high-throughput hematotoxicity screening and testing with its proprietary HALO®-Tox HT Platform. Provides the expertise to help in predicting toxicity, risk and safety of a drug or other agent. | stem cell testing, in vitro toxicity screening, hematotoxicity screening and testing, predicting toxicity, | SCR_028449 | 2026-08-12 10:54:20 | 0 | ||||||||||||
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GATK VariantFiltration Resource Report Resource Website 1+ mentions |
GATK VariantFiltration (RRID:SCR_028441) | software resource, software application | 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 | hard-filtering variant callsets, annotate low-quality variants, |
is related to: GATK is organization facet of: Broad Institute |
Free, Freely available | https://gatk.broadinstitute.org/hc/en-us | SCR_028441 | 2026-08-12 10:54:09 | 1 | |||||||||
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bedGraphToBigWig Resource Report Resource Website 1+ mentions |
bedGraphToBigWig (RRID:SCR_028439) | software resource, software application | 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. | Convert bedGraph file to bigWig format, convert text-based bedGraph files, indexed binary bigWig files, transform genome coverage data, |
is related to: BigWig and BigBed works with: UCSC Genome Browser |
DOI:10.1093/bioinformatics/btq351 | Free, Freely available, | SCR_028439 | 2026-08-12 10:54:00 | 3 | |||||||||
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Membrane Protein-Lipid Interaction Database Resource Report Resource Website |
Membrane Protein-Lipid Interaction Database (RRID:SCR_028506) | MPLID | data or information resource, database, software resource, source code | Database for residue-level membrane protein-lipid contact annotations derived from experimentally determined Protein Data Bank structures. Includes automated Python pipeline for identifying lipid-containing PDB structures, calculating all-atom heavy-atom residue-lipid contacts using a 4.0 Angstrom distance cutoff, generating cluster-aware train, validation, and test splits, and producing documented dataset files for machine learning and structural bioinformatics. The dataset is deposited on Zenodo under CC0, while the code is released on GitHub under the MIT license. Contains large-scale experimentally-validated dataset of residue-level protein-lipid contacts from membrane protein structures. | large-scale experimentally-validated dataset, residue-level protein-lipid contacts, membrane protein structures, | Free, Available for download, Freely available | SCR_028506 | MPLID: Membrane Protein-Lipid Interaction Database | 2026-08-12 10:54:01 | 0 | |||||||||
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Modbamtools Resource Report Resource Website |
Modbamtools (RRID:SCR_028809) | software toolkit, software resource, source code | Software tools to visualize methylation data using bam file. Used to manipulate and visualize modified base bam files. | methylation data, bam file, visualize methylation data using bam file, manipulate and visualize modified base bam files, | Free, Available for download, Freely available | SCR_028809 | modbamtools | 2026-08-12 10:54:23 | 0 |
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