Tools   Select Another Resource Report Type

https://www.freecad.org/

Open source parametric 3D modeler to design real life objects of any size. Parametric modeling allows modify your design by going back into your model history and changing its parameters.

Proper citation: FreeCAD (RRID:SCR_022535) Copy   

•   Source: SciCrunch Registry

https://github.com/kalininalab/d-StructMAn

Software tool provides annotation of non-synonymous single nucleotide variants in context of structural properties of resulting amino acid changes in corresponding proteins. Improved implementation of StructMAn, shipped in container form and extended to annotation of short in-frame indels and alterations arising as consequence of alternative splicing events. Produces range of structural features by combining information from experimentally resolved structures of many related proteins, which is unique feature of StructMAn family tools. Can also harness all protein structure models stored in AlphaFold Protein Structure Database.

Proper citation: d-StructMAn (RRID:SCR_022534) Copy   

•   Source: SciCrunch Registry

https://github.com/Hi5App

Software cross platform mobile application that supports 2D/3D/4D image visualization, multi-morphometry annotation, proofreading, interactive imaging system controlling, and distributed collaboration.

Proper citation: Hi5App (RRID:SCR_022819) Copy   

•   Source: SciCrunch Registry

https://github.com/replikation/What_the_Phage

Parallel multitool approach for phage prediction combined with annotation and classification downstream strategy. Used for identification and analysis of phage sequences. Phage identification via nextflow and docker or singularity.

Proper citation: What the Phage (RRID:SCR_022871) Copy   

•   Source: SciCrunch Registry

https://github.com/SydneyBioX/SurvBenchmark_package

Software package for comprehensive benchmarking study of survival analysis methods using both omics data and clinical data. Evaluates diverse collection of survival models for both clinical and omics datasets.

Proper citation: SurvBenchmark (RRID:SCR_022503) Copy   

•   Source: SciCrunch Registry

https://github.com/h2oai/h2o4gpu

Interface to H2O4GPU, collection of GPU solvers for machine learning algorithms.

Proper citation: h2o4gpu (RRID:SCR_022520) Copy   

•   Source: SciCrunch Registry

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

Software R package Themes for use with Shiny.

Proper citation: shinythemes (RRID:SCR_022757) Copy   

•   Source: SciCrunch Registry

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

Software R package to add markdown helpfiles to shiny apps, using modal dialog boxes, with no need to observe each help button separately.

Proper citation: shinyhelper (RRID:SCR_022755) Copy   

•   Source: SciCrunch Registry

https://bids-matlab.readthedocs.io/en/latest/

Software MATLAB/Octave tools to interact with datasets conforming to Brain Imaging Data Structure format.

Proper citation: BIDS-Matlab (RRID:SCR_022292) Copy   

•   Source: SciCrunch Registry

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

Software R package providing missing functionality to ggplot2 through extension system introduced with ggplot2 v2.0.0.

Proper citation: ggforce (RRID:SCR_022575) Copy   

•   Source: SciCrunch Registry

https://github.com/ZhiGroup/IBD_benchmark

Software package as open source project benchmarks IBD detection tools with multiple measurements.

Proper citation: IBD Detection Tool Benchmark Tool (RRID:SCR_022850) Copy   

•   Source: SciCrunch Registry

https://github.com/anuprulez/ml-jupyter-notebook

Open source, docker based, and GPU enabled jupyterlab notebook infrastructure that runs on public compute infrastructure of Galaxy Europe for rapid prototyping and developing end-to-end AI projects. Jupyterlab notebook in GPU enabled docker container for machine learning and deep learning.

Proper citation: Docker based GPU enabled Jupyterlab (RRID:SCR_022695) Copy   

•   Source: SciCrunch Registry

http://cns.hkbu.edu.hk/RIDE.htm

Software Matlab based toolbox for temporal decomposition of EEG signal. Used for decomposition, reconstruction, and single trial analysis of event related potentials.

Proper citation: Residue Iteration Decomposition (RRID:SCR_022174) Copy   

•   Source: SciCrunch Registry

https://github.com/alexcwsmith/PiRATeMC

Software data management pipeline for camera synchronization and combined data directories.

Proper citation: Pi-based Remote Acquisition Technology for Motion Capture (RRID:SCR_022327) Copy   

•   Source: SciCrunch Registry

https://jarvis-mocap.github.io/jarvis-docs/

Software markerless 3D motion capture toolbox. Used for capturing precise 3D motion.

Proper citation: Joint Acquisition, Recording and Voxel based Inference System (RRID:SCR_022723) Copy   

•   Source: SciCrunch Registry

https://github.com/Frederik-D-Weber/zmax_edf_merge_converter

Software tool for comprehensive conversion of folder with Hypnodyne zmax EDF files into merged European Data Format.

Proper citation: zmax_edf_merge_converter (RRID:SCR_022567) Copy   

•   Source: SciCrunch Registry

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

Software R package implementation of cumulative link models also known as ordered regression models, proportional odds models, proportional hazards models for grouped survival times and ordered logit/probit models.

Proper citation: ordinal (RRID:SCR_022856) Copy   

•   Source: SciCrunch Registry

https://github.com/ggruenhagen3/coselens

Software R package to detect gene level differential selection between two groups of samples.Used for calculation of excess of non synonymous mutations between two groups.

Proper citation: Coselens (RRID:SCR_022578) Copy   

•   Source: SciCrunch Registry

https://github.com/tlancian/bio_cs

Software package for implementing algorithms proposed in Lanciano et al. "Contrast Subgraphs Allow Comparing Homogeneous and Heterogeneous Networks Derived from Omics Data".

Proper citation: bio_contrast_subgraph (RRID:SCR_022853) Copy   

•   Source: SciCrunch Registry

https://github.com/HChai01/ISGPRE

Software package for predicting interferon stimulated human genes.

Proper citation: ISGPRE (RRID:SCR_022730) Copy   

•   Source: SciCrunch Registry