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https://www.nitrc.org/search/?type_of_search=group&q=wisconsin&sa.x=0&sa.y=0&sa=Search

Atlases enable alignment of individual scans to improve localization and statistical power of results, and allow comparison of results between studies and institutions. Set of multi subject atlas templates is constructed specifically for functional and structural imaging studies of rhesus macaque.

Proper citation: Rhesus Macaque Brain Atlases (RRID:SCR_017533) Copy   

•   Source: SciCrunch Registry

http://reproducibility.stanford.edu/

Center with the goal of harnessing high-performance computing to make neuroscience research more reliable.Provide researchers with tools to analyze their data in ways that focus on the reproducibility of the results through the OpenfMRI ( OpenNeuro ) and Neurovault projects.

Proper citation: Stanford Center for Reproducible Neuroscience (RRID:SCR_016684) Copy   

•   Source: SciCrunch Registry

https://github.com/kstreet13/slingshot

Software R package for identifying and characterizing continuous developmental trajectories in single cell data. Cell lineage and pseudotime inference for single-cell transcriptomics.

Proper citation: Slingshot (RRID:SCR_017012) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

https://github.com/BodenmillerGroup/imctools

Software Python package that implements preprocessing pipeline for imaging mass cytometry data. Can convert IMC raw files to tiff files that are used as inputs into CellProfiller, Ilastik, Fiji etc.

Proper citation: imctools (RRID:SCR_017132) Copy   

•   Source: SciCrunch Registry

https://github.com/colinvaz/nmf-toolbox

Software toolbox for performing Non-negative Matrix Factorization (NMF) and several variants. Used to factorize one non negative matrix into two non negative factors, that is basis matrix and coefficient matrix. Applied in bioinformatics as data mining approach.

Proper citation: NMF Toolbox (RRID:SCR_017069) Copy   

•   Source: SciCrunch Registry

https://github.com/AlexsLemonade/refinebio

Software tool to uniformly process and normalize large amounts of data. Harmonizes petabytes of publicly available biological data into ready-to-use datasets for cancer researchers and AI/ML scientists.

Proper citation: refine.bio (RRID:SCR_017471) Copy   

•   Source: SciCrunch Registry

http://www.biosoft.com/w/assayzap.htm

Software tool as universal assay calculator for RIA, ELISA, IRMA, colorimetric or any other type of assay by Biosoft. Maintains record for each assay, and enables standard curve and QCs to be compared and adjusted. Can process data from 96 and 384-well plate readers in any order.

Proper citation: AssayZap (RRID:SCR_016991) Copy   

•   Source: SciCrunch Registry

http://hmri.info

Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis.

Proper citation: hMRI-toolbox (RRID:SCR_017682) Copy   

•   Source: SciCrunch Registry

https://github.com/hemberg-lab/scmap

Software tool for unsupervised projection of single cell RNA-seq data. Used for projecting cells from scRNA-seq data set onto cell types or individual cells from other experiments.

Proper citation: Scmap (RRID:SCR_017338) Copy   

•   Source: SciCrunch Registry

https://github.com/taborlab/FlowCal

Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots.

Proper citation: FlowCal (RRID:SCR_018140) Copy   

•   Source: SciCrunch Registry

https://github.com/Nevermore520/NeuronTools

Software tools for converting data files into persistence diagrams and distance matrices.

Proper citation: Neuron Tools (RRID:SCR_017450) Copy   

•   Source: SciCrunch Registry

https://github.com/wdecoster/nanofilt

Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data.

Proper citation: NanoFilt (RRID:SCR_016966) Copy   

•   Source: SciCrunch Registry

https://github.com/mandricigor/ScaffMatch

Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes.

Proper citation: ScaffMatch (RRID:SCR_017025) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/nicofmay/basta-bayesian-structured-coalescent-approximation/src/master/

Software package as Bayesian method to infer migration from genetic data. Implemented in BEAST2 that combines accuracy of methods based on structured coalescent with computational efficiency required to handle more than few populations.

Proper citation: BASTA (RRID:SCR_017303) Copy   

•   Source: SciCrunch Registry

https://scienceofbehaviorchange.org/about/

Repository for behavioral science measures that have been validated or are in process of being validated in accordance with SOBC Experimental Medicine Approach.

Proper citation: Science of Behavior Change Research Network (RRID:SCR_017385) Copy   

•   Source: SciCrunch Registry

https://geomagic-studio.software.informer.com/12.0/

Software tool to convert 3D scans into parametric models. Transforms 3D scan data into highly accurate surface, polygon and native CAD models. Used for reverse engineering, product design, rapid prototyping and analysis.

Proper citation: GEOMAGIC Studio (RRID:SCR_016978) Copy   

•   Source: SciCrunch Registry

https://kona.nhgri.nih.gov/mnemiopsis/

Portal to obtain genomic information on Mnemiopsis. Data available provide annotations and other key biological information not available elsewhere. Used to advance research projects aimed at understanding phylogenetic diversity and evolution of proteins that play fundamental role in metazoan development. Collection of sequenced, assembled, annotated, and performed preliminary analysis of genome of Mnemiopsis.

Proper citation: Mnemiopsis Genome Project Portal (RRID:SCR_018293) Copy   

•   Source: SciCrunch Registry

https://hdmf.readthedocs.io/

Open source software Python package for working with hierarchical data. Provides APIs for specifying data models, reading and writing data to different storage backends, and representing data with Python object.Used for working with standardizing, reading, and writing hierarchical object data.

Proper citation: Hierarchical Data Modeling Framework (RRID:SCR_021303) Copy   

•   Source: SciCrunch Registry

https://rubygems.org/gems/viral_seq

Ruby Gem with bioinformatics tools for processing viral NGS data. Specifically for Primer-ID sequencing and HIV drug resistance analysis.

Proper citation: viral_seq (RRID:SCR_018515) Copy   

•   Source: SciCrunch Registry

https://github.com/berenslab/EphysExtraction

Software tool as code to extract electrophysiological parameters of neurons. Code is continuously being updated to handle more kinds of voltage traces and extract different kinds of features.

Proper citation: EphysExtraction (RRID:SCR_018193) Copy   

•   Source: SciCrunch Registry