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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

https://github.com/AntonioDeFalco/SCEVAN

Software R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.

Proper citation: SCEVAN (RRID:SCR_028766) Copy   

•   Source: SciCrunch Registry

https://www.menarinisiliconbiosystems.com

Biotechnology and diagnostics company specializing in "liquid biopsy" technologies to detect and isolate rare cells like circulating tumor cells (CTCs) from blood or tissue samples. They provide precise single-cell analysis tools used in cancer research and personalized medicine. Offers commercial rare-cell laboratory service providing CD138-positive immunomagnetic enrichment of plasma cells from peripheral blood and immunofluorescence-based plasma-cell identification and enumeration, delivering an enriched circulating multiple myeloma cell fraction for downstream analysis.

Proper citation: Menarini Silicon Biosystems Inc (RRID:SCR_028704) 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://www.bio-rad.com/en-us/product/qx600-droplet-digital-pcr-system?ID=b07d12ac-0585-fc4c-a586-3ddf20d5c4a0

Advanced laboratory instrument used for absolute quantification of DNA and RNA. It partitions samples into 20,000 nanoliter sized droplets and uses 6-color multiplexing to test up to 12 targets per well with high sensitivity.

Proper citation: Bio-Rad: QX600 Droplet Digital PCR System (RRID:SCR_028830) Copy   

•   Source: SciCrunch Registry

https://github.com/Arcadia-Science/glass-box-umap

Software Python package for making UMAP interpretable with exact feature contributions. Used to explain why data points land in specific places on a UMAP map. Augments UMAP by computing exact feature contributions to the UMAP embedding. Standard UMAP produces embeddings but offers no insight into why points land where they do. Glass Box UMAP solves this by using a specially designed neural network that enables exact computation of feature contributions, and does so without approximations. The feature contributions are mathematically exact, validated to near machine precision.

Proper citation: Glass Box UMAP (RRID:SCR_028826) Copy   

•   Source: SciCrunch Registry