Tools   Select Another Resource Report Type

https://www.graham-center.org/maps-data-tools/social-deprivation-index.html

SDI is composite measure of area level deprivation based on seven demographic characteristics collected in the American Community Survey and used to quantify the socio-economic variation in health outcomes.

Proper citation: Social Deprivation Index (RRID:SCR_025026) 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://fsl.fmrib.ox.ac.uk/fsl/fslwiki/baycest

Software tool for Bayesian analysis for chemical exchange saturation transfer z-spectra.

Proper citation: BayCEST (RRID:SCR_024951) 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://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Fslutils

Software application set of useful command line utilities which allow conversion, processing etc. of Analyze and Nifti format data sets.

Proper citation: Fslutils (RRID:SCR_024943) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Atlasquery

Software tool designed to allow command line interrogation of atlas images supplied with FSL. It takes as input the name of one of FSL atlases together with either coordinate of interest or mask.

Proper citation: Atlasquery (RRID:SCR_024944) 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://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ICA_PNM

Software de-noising pipeline combines noise regressors identified by tools such as PNM and ICA (and FIX) and effectively prepares them for entry into single FEAT model, thus allowing the user to clean data in single step.

Proper citation: ICA-PNM (RRID:SCR_024952) 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://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Cluster

Software application used to form clusters, report information about clusters and/or perform cluster based inference.

Proper citation: fsl-cluster (RRID:SCR_024938) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/XTRACT

Software command line tool for automated tractography. Standardised protocols for automated tractography in human and macaque brain.

Proper citation: XTRACT (RRID:SCR_024933) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/eddy

Software tool for correcting eddy currents and movements in diffusion data. Used to predict undistorted data, to which actual observed images can be aligned, to estimate and to correct for volume-to-volume movement and off-resonance fields, to signal dropout caused by movement during diffusion encoding, within-volume movement and movement-induced changes of susceptibility-induced off-resonance field. In addition to correcting for these effects, the output from this framework offers description of off resonance and subject movement effects present in uncorrected data.

Proper citation: eddy (RRID:SCR_024934) Copy   

•   Source: SciCrunch Registry

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/Randomise

Software tool for nonparametric permutation inference on neuroimaging data.

Proper citation: randomise (RRID:SCR_024937) Copy   

•   Source: SciCrunch Registry

https://broadinstitute.github.io/warp/docs/Pipelines/snm3C/README

Software open-source, cloud-optimized computational workflow for processing single-nucleus methylome and chromatin contact (snm3C) sequencing data. The workflow is designed to demultiplex and align raw sequencing reads, call chromatin contacts, and generate summary metrics.

Proper citation: snm3C Pipeline (RRID:SCR_025041) 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

http://www.ldbase.org

NIH funded collaboration between researchers and librarians to build behavioral project oriented data repository containing decades of knowledge from educational and developmental sciences on individuals across the full range of abilities.

Proper citation: LDbase (RRID:SCR_025052) 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/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://www.npatlas.org

Open access knowledge base for microbial natural products discovery. Database of microbially derived natural product structures. Provides coverage of bacterial and fungal natural products to visualize chemical diversity. Includes compounds and contains referenced data for structure, compound names, source organisms, isolation references, total syntheses, and instances of structural reassignment. Interactive web portal permits searching by structure, substructure, and physical properties. Provides mechanisms for visualizing natural products chemical space and dashboards for displaying author and discovery timeline data. Atlas has been developed under FAIR principles.

Proper citation: Natural Products Atlas (RRID:SCR_025107) Copy   

•   Source: SciCrunch Registry

https://imagej.net/plugins/jacop

Software toolbox as plugin for ImageJ that supports colocalization analysis in light microscopy. Used for subcellular colocalization analysis under ImageJ that integrates current global statistic methods and novel object-based approach.

Proper citation: JaCoP (RRID:SCR_025164) Copy   

•   Source: SciCrunch Registry