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https://biostat.app.vumc.org/wiki/Main/PowerSampleSize

Software application as interactive program for performing power and sample size calculations. Can determine the sample size needed to detect specified alternative hypothesis with required power, the power with which specific alternative hypothesis can be detected with given sample size, or the specific alternative hypotheses that can be detected with given power and sample size.

Proper citation: PS:Power and Sample Size Calculation (RRID:SCR_024912) Copy   

•   Source: SciCrunch Registry

http://daphnia.io/

Whole organism atlas utilizing 2D and 3D imaging. Atlas at cellular resolution serves as foundation for characterization of tissue and cellular change in Daphnia.

Proper citation: Daphnia Atlas (RRID:SCR_024913) Copy   

•   Source: SciCrunch Registry

https://github.com/xinhe-lab/GSFA

Software R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single cell CRISPR screening data.

Proper citation: Guided Sparse Factor Analysis (RRID:SCR_025023) Copy   

•   Source: SciCrunch Registry

https://www.rdocumentation.org/packages/gplots/versions/3.1.3.1

Software R package to create figures.

Proper citation: gplots (RRID:SCR_025035) Copy   

•   Source: SciCrunch Registry

https://github.com/dattalab/moseq2-app

Software application as starting point to MoSeq2 package suite. Unsupervised machine learning method which takes inputs from depth cameras in 3D and transforms them into different behavioral motifs which called syllables. Used to extract mouse pose from depth video and model how pose evolves over time.

Proper citation: moseq2-app (RRID:SCR_025031) Copy   

•   Source: SciCrunch Registry

https://github.com/EtieM/outLyzer

Software tool for extracting low-allele-frequency tumor mutations from sequencing background noise in clinical practice. Detects variations, specifically low allele frequency variation, in next generation sequencing data.

Proper citation: OutLyzer (RRID:SCR_025120) Copy   

•   Source: SciCrunch Registry

https://sites.google.com/site/plaresmedima/

Software tool to support translation of basic research in medical image analysis into early clinical studies.

Proper citation: PMI (RRID:SCR_025084) Copy   

•   Source: SciCrunch Registry

https://github.com/BlankenbergLab/gmxtras/tree/main

Software tool as set of Python scripts to modify GROMACS topology files, by adding content from different topology files and other GROMACS input files. Useful, particularly when system components are assembled outside of GROMACS, or in different steps within GROMACS. This helps prevent users from having to copy and paste significantly large blocks of text within topology files.

Proper citation: GROMACS topology editors (RRID:SCR_025013) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=nricens

Software R package for calculating Net Reclassification Improvement for risk prediction models with time to event and binary data. NRI for risk prediction models with time to event and binary response data.

Proper citation: nricens (RRID:SCR_025138) Copy   

•   Source: SciCrunch Registry

https://github.com/luo-xiaolong/GSC

Software tool for lossless compression of VCF files, designed to efficiently store and manage VCF files in compressed format. It accepts VCF/BCF files as input and utilizes advanced compression techniques to significantly reduce storage requirements while ensuring fast query capabilities.

Proper citation: Genotype Sparse Compression (RRID:SCR_025071) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=ggsurvfit

Software R package for flexible time-to-event figures creation. Used to create figures ready for publication.

Proper citation: ggsurvfit (RRID:SCR_025045) Copy   

•   Source: SciCrunch Registry

https://numba.readthedocs.io/en/stable/index.html

Open source JIT compiler that translates subset of Python and NumPy code into fast machine code. Can compile large subset of numerically-focused Python, including many NumPy functions. Has support for automatic parallelization of loops, generation of GPU-accelerated code, and creation of ufuncs and C callbacks.

Proper citation: Numba (RRID:SCR_025056) Copy   

•   Source: SciCrunch Registry

https://www.3ds.com/products/simulia/abaqus

Software suite for finite element analysis and computer aided engineering.

Proper citation: Abaqus FEA (RRID:SCR_024997) Copy   

•   Source: SciCrunch Registry

https://github.com/aprismatic/prismadb

Software application as cryptographic security layer for relational database systems, that currently supports Microsoft SQL Server, MySQL, MariaDB, PostgreSQL and CockroachDB. Security layer for relational database systems.

Proper citation: Prisma/DB (RRID:SCR_025246) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=gridExtra

Softwate R package to work with "grid" graphics, notably to arrange multiple grid-based plots on page, and draw tables. Miscellaneous functions for Grid graphics.

Proper citation: gridExtra (RRID:SCR_025249) Copy   

•   Source: SciCrunch Registry

https://github.com/yichun10/bioKGQA-KGT.git

Software contains all scripts and instructions for running Knowledge Graph-based Thought model, which is knowledge graph enhanced LLMs framework for pan-cancer question answering.

Proper citation: bioKGQA-KGT (RRID:SCR_025176) Copy   

•   Source: SciCrunch Registry

https://github.com/kryptnostic/krypto

Software C++ implementation of multivariate quadratic FHE.

Proper citation: krypto (RRID:SCR_025179) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/sysbiobig/movarsim

Software simulator that leverages data-driven information to set both variants and reads characteristics, producing realistic tumoral samples. Computational modelling of cancer-specific variants and sequencing reads characteristics for realistic tumoral sample simulation.

Proper citation: MOVARSim (RRID:SCR_025388) Copy   

•   Source: SciCrunch Registry

https://lambada.icm-institute.org

Reference atlas of the developing post-natal mouse brain. Provides data and annotations on distribution of cells and gene expression in mouse brain.

Proper citation: LAMBADA (RRID:SCR_025382) Copy   

•   Source: SciCrunch Registry

https://github.com/PhysiCell-Tools/PhysiCell-Studio

Software graphical tool to allow easy editing of (XML) model, create initial positions of cells, run simulation, and visualize results. To contribute, fork and make PRs to the development branch. Used to create, execute, and visualize multicellular model using PhysiCell.

Proper citation: PhysiCell Studio (RRID:SCR_025311) Copy   

•   Source: SciCrunch Registry