Tools   Select Another Resource Report Type

https://github.com/lda-project/lda

Software application for topic modeling with latent Dirichlet allocation.

Proper citation: lda (RRID:SCR_027850) Copy   

•   Source: SciCrunch Registry

https://opensourcephysics.github.io/tracker-website/

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.

Proper citation: Tracker (RRID:SCR_027845) Copy   

•   Source: SciCrunch Registry

https://github.com/brain-bican/developing_human_brain_atlas_ontology

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.

Proper citation: Developmental Human Brain Atlas Ontology (DHBA) (RRID:SCR_027940) Copy   

•   Source: SciCrunch Registry

https://bican-bg.vercel.app/

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.

Proper citation: BICAN Basal Ganglia Epigenome Explorer (RRID:SCR_027887) Copy   

•   Source: SciCrunch Registry

https://github.com/NOW-Lab/STICR

Code to conduct combinatorial barcoding. scRNA-seq-compatible tracer for identifying clonal relationships.

Proper citation: STICR (RRID:SCR_027856) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/sivic/

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.

Proper citation: Spectroscopic Imaging, VIsualization, and Computing (SIVIC) (RRID:SCR_027875) Copy   

•   Source: SciCrunch Registry

https://purr.purdue.edu

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.

Proper citation: Purdue University Research Repository (PURR) (RRID:SCR_027877) Copy   

•   Source: SciCrunch Registry

https://alleninstitute.github.io/scrattch.taxonomy/

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

Proper citation: scrattch taxonomy (RRID:SCR_027910) Copy   

•   Source: SciCrunch Registry

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

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.

Proper citation: DMRcate (RRID:SCR_028007) Copy   

•   Source: SciCrunch Registry

https://github.com/capuccino26/POLY_PIPELINE

Software data analysis pipeline for spatial transcriptomics data tailored to polyploid organisms.

Proper citation: Poly Pipeline (RRID:SCR_027993) Copy   

•   Source: SciCrunch Registry

https://github.com/ZhuoliHuang/CIMA_BMI_paper

Source analysis and data processing code for article titled "Single-Cell Multi-Omics Insights into BMI-Mediated Immune-Related Disease Risk".

Proper citation: CIMA_BMI_paper (RRID:SCR_028241) Copy   

•   Source: SciCrunch Registry

https://github.com/brentp/somalier

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.

Proper citation: somalier (RRID:SCR_028167) Copy   

•   Source: SciCrunch Registry

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://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://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://www.hemogenix.com/

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.

Proper citation: HemoGenix (RRID:SCR_028449) 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://github.com/omagebright/MPLID

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.

Proper citation: Membrane Protein-Lipid Interaction Database (RRID:SCR_028506) Copy   

•   Source: SciCrunch Registry

https://github.com/rrazaghi/modbamtools

Software tools to visualize methylation data using bam file. Used to manipulate and visualize modified base bam files.

Proper citation: Modbamtools (RRID:SCR_028809) Copy   

•   Source: SciCrunch Registry