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https://github.com/carmonalab/ProjecTILs

Software tool to project scRNA-seq data into reference single-cell atlases, enabling their direct comparison in stable, annotated system of coordinates. Predicts effects of cell perturbations and identifies gene programs that are altered in different conditions and tissues. Used for interpretation of cell states using reference single-cell maps.

Proper citation: projecTILs (RRID:SCR_026854) Copy   

•   Source: SciCrunch Registry

https://github.com/BGI-shenzhen/RectChr

Software tool for multi-level visualization of genomic statistical variables on rectangular chromosomes.

Proper citation: RectChr (RRID:SCR_026859) Copy   

•   Source: SciCrunch Registry

https://github.com/james-cole/brainageR

Software R tool for generating brain-predicted age value, using Gaussian Processes regression. Used for generating brain-predicted age value from raw T1-weighted MRI scan.

Proper citation: brainageR (RRID:SCR_026826) Copy   

•   Source: SciCrunch Registry

https://github.com/Rosemeis/pcangsd

Software framework for analyzing low-depth next-generation sequencing data in heterogeneous/structured populations using principal component analysis.

Proper citation: pcangsd (RRID:SCR_026956) Copy   

•   Source: SciCrunch Registry

https://github.com/DerrickWood/kraken2

Software tool as second version of Kraken taxonomic sequence classification system.

Proper citation: kraken2 (RRID:SCR_026838) Copy   

•   Source: SciCrunch Registry

https://github.com/BigDataBiology/SemiBin/

Software command tool for metagenomic binning with deep learning, handles both short and long reads. Used for metagenomic binning at contig level which uses deep contrastive learning.

Proper citation: SemiBin (RRID:SCR_026896) Copy   

•   Source: SciCrunch Registry

https://github.com/chklovski/CheckM2

Software tool to predict completeness and contamination of genomic bins. Used for predicting genome quality of metagenome-assembled genomes. Assessing microbial genome quality using machine learning.

Proper citation: CheckM2 (RRID:SCR_026897) Copy   

•   Source: SciCrunch Registry

https://github.com/qcxms/QCxMS

Software application as quantum chemical based program that enables users to calculate mass spectra using Born-Oppenheimer Molecular Dynamics. Quantum mechanic mass spectrometry calculation program.

Proper citation: QCxMS (RRID:SCR_026928) Copy   

•   Source: SciCrunch Registry

https://github.com/OpenTOPAS/OpenTOPAS

Software Monte Carlo tool for particle simulation. Used for simulation of medical applications of ionizing radiation with the Monte Carlo method. Allows to assemble and control library of simulation objects (geometry components, particle sources, scorers, etc.) with no need to write C++ code and without knowledge of underlying Geant4 Simulation Toolkit.

Proper citation: OpenTOPAS (RRID:SCR_026927) Copy   

•   Source: SciCrunch Registry

https://github.com/gevaertlab/DUNE

Software tool to extract low-dimensional deep features from multisequence brain MRI data using unsupervised autoencoders.

Proper citation: GevaertLab_DUNE (RRID:SCR_027208) Copy   

•   Source: SciCrunch Registry

https://opendata.cbs.nl/#/CBS/nl/dataset/85457NED

Database of Statistics Netherlands (CBS). Contains lifestyle data of Dutch population living in private households. The numbers can be broken down by various personal characteristics.

Proper citation: CBS StatLine - Lifestyle (RRID:SCR_027121) Copy   

•   Source: SciCrunch Registry

https://github.com/Danko-Lab/dREG

Software tool for detecting regulatory elements using GRO-seq and PRO-seq.

Proper citation: dREG (RRID:SCR_027012) Copy   

•   Source: SciCrunch Registry

https://github.com/steineggerlab/foldseek

Software tool for fast and sensitive comparisons of large structure sets. Used for comparisons of large protein structure sets, supporting monomer and multimer searches, as well as clustering. It runs on CPU, supports GPU acceleration for faster searches, and optionally allows ultra-fast and sensitive comparisons directly from protein sequence inputs using a language model, bypassing the need for structures.

Proper citation: Foldseek (RRID:SCR_027018) Copy   

•   Source: SciCrunch Registry

https://github.com/yichun10/BioCDQA.git

Software retrieval-augmented knowledge mining method with deep thinking LLMs for biomedical research and clinical support. Cross-document question answering dataset addressing current QA limitations, and features Progressive Retrieval-Augmented Reasoning framework that combines advanced retrieval-generation techniques with self-reflection mechanisms and deep-thinking large language models to enhance answer accuracy and contextual relevance.Used to evaluate latent knowledge retrieval and multi-hop reasoning capabilities.

Proper citation: BioCDQA (RRID:SCR_027068) Copy   

•   Source: SciCrunch Registry

https://github.com/qiankunzizairen/PanGIA

Software tool for predicting ncRNA-disease associations. Used for identifying association between ncRNAs and diseases.

Proper citation: PanGIA (RRID:SCR_027069) Copy   

•   Source: SciCrunch Registry

https://github.com/jorgemasgomez/almondcv2

Software repository provides open-source implementation of RGB imaging workflow for morphological and morphometric analysis of fruits and seeds.

Proper citation: almondcv2 (RRID:SCR_027064) Copy   

•   Source: SciCrunch Registry

https://github.com/mskcc/vcf2maf

Software tool to convert Virtual Contact File into Mutation Annotation Format, where each variant is annotated to only one of all possible gene isoforms.

Proper citation: vcf2maf (RRID:SCR_027063) Copy   

•   Source: SciCrunch Registry

https://www.meshlab.net/

Software application used for processing and editing 3D triangular meshes. Provides tools for editing, cleaning, repairing, inspecting, rendering, texturing, and converting meshes. This makes it suitable for variety of tasks related to 3D data, including preparing models for 3D printing.

Proper citation: Meshlab (RRID:SCR_027065) Copy   

•   Source: SciCrunch Registry

https://github.com/dpeerlab/Palantir/

Algorithm to align cells along differentiation trajectories. Models trajectories of differentiating cells by treating cell fate as probabilistic process and leverages entropy to measure cell plasticity along the trajectory. Generates high-resolution pseudo-time ordering of cells and, for each cell state, assigns probability of differentiating into each terminal state.

Proper citation: Palantir (RRID:SCR_027194) Copy   

•   Source: SciCrunch Registry

https://www.merative.com/real-world-evidence/real-world-data-analytics#skiptheform-marketscan

Employer-sourced medical and drugs claims database of the under-65 working population and their dependents, as well as 65+ with Medicare supplemental insurance paid by employers.

Proper citation: MarketScan by Merative (RRID:SCR_027329) Copy   

•   Source: SciCrunch Registry