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

Object-oriented software for model-robust covariance matrix estimators. Starting out from the basic robust Eicker-Huber-White sandwich covariance methods include: heteroscedasticity-consistent (HC) covariances for cross-section data; heteroscedasticity- and autocorrelation-consistent (HAC) covariances for time series data (such as Andrews' kernel HAC, Newey-West, and WEAVE estimators); clustered covariances (one-way and multi-way); panel and panel-corrected covariances; outer-product-of-gradients covariances; and (clustered) bootstrap covariances. All methods are applicable to (generalized) linear model objects fitted by lm() and glm() but can also be adapted to other classes through S3 methods.

Proper citation: sandwich (RRID:SCR_027691) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/uniluxembourg/lcsb/systems-ecology/pathofact2

Software integrative pipeline for antimicrobial resistance genes, virulence factors, toxins, and biosynthetic gene clusters prediction in metagenomes. Used for predicting microbiome-based pathogenicity and resistance to better understand and address challenges posed by antimicrobial resistance and infectious diseases.

Proper citation: PathoFact2 (RRID:SCR_027650) Copy   

•   Source: SciCrunch Registry

https://www.microchip.com/en-us/tools-resources/develop/mplab-x-ide

Software program from Microchip, serving as a comprehensive, expandable platform for developing Microchip microcontroller applications, with many integrated tools like MPLAB Code Configurator (MCC) and MPLAB XC Compilers (free versions). Incorporates tools to discover, configure, develop, debug and qualify embedded designs for most of microcontrollers and digital signal controllers. MPLAB X IDE works seamlessly with the MPLAB development ecosystem of software and tools.

Proper citation: mplab x ide (RRID:SCR_027844) Copy   

•   Source: SciCrunch Registry

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://cran.r-project.org/src/contrib/Archive/peakPick/

Software R package for identifying peaks in data related to genomics, genetics, or epigenetics research.

Proper citation: peakPick (RRID:SCR_027740) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/llm-pathway-curator/

Software quality-assurance layer for pathway enrichment interpretation that converts enrichment term lists into context-conditioned, evidence-linked, schema-bounded claims and assigns PASS/ABSTAIN/FAIL via predefined, rule-based audit gates (stability, context validity stress tests, evidence-link integrity, and contradiction checks), producing decision-grade reports with audit logs. The LLM is confined to proposal-only steps; final decisions are mechanical and reproducible.

Proper citation: LLM-PathwayCurator (RRID:SCR_027964) 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://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://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/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://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://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://simtk.org/home/simbody

This project is a SimTK Core toolset providing general multibody dynamics capability, i.e., the capability to solve Newton's 2nd law F=ma in any set of coordinates. The techniques of rigid body mechanics are used to provide results in Order(n) time for any set of n coordinates. This can be used for internal coordinate modeling of molecules, or for coarse-grained models based on larger chunks. It is also useful for large-scale mechanical models, such as neuromuscular models of human gait. Simbody is provided as an open source, object-oriented C++ API and delivers high-performance, accuracy-controlled science/engineering-quality results. Binaries of this software are bundled with other SimTK Core modules.

Proper citation: Simbody(tm): SimTK Multibody Dynamics Toolset (RRID:SCR_002684) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/pirs/

Software for de novo data simulation. It uses empirical distribution to reproduce Illumina pair-end reads with real distribution of substitution sequencing errors, quality values and GC%-depth bias.

Proper citation: pIRS (RRID:SCR_002519) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/panda-tool/

Software matlab toolbox for pipeline processing of diffusion MRI images. For each subject, PANDA can provide outputs in 2 types: i) diffusion parameter data that is ready for statistical analysis; ii) brain anatomical networks constructed by using diffusion tractography. Particularly, there are 3 types of resultant diffusion parameter data: WM atlas-level, voxel-level and TBSS-level. The brain network generated by PANDA has various edge definitions, e.g. fiber number, length, or FA-weighted. The key advantages of PANDA are as follows: # fully-automatic processing from raw DICOM/NIFTI to final outputs; # Supporting both sequential and parallel computation. The parallel environment can be a single desktop with multiple-cores or a computing cluster with a SGE system; # A very friendly GUI (graphical user interface).

Proper citation: PANDA (RRID:SCR_002511) Copy   

•   Source: SciCrunch Registry

http://briansimulator.org/

Software Python package for simulating spiking neural networks. Useful for neuroscientific modelling at systems level, and for teaching computational neuroscience. Intuitive and efficient neural simulator.

Proper citation: Brian Simulator (RRID:SCR_002998) Copy   

•   Source: SciCrunch Registry