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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
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
https://openwetware.org/wiki/HughesLab:JTK_Cycle
Software R package for Detecting Rhythmic Components in Genome-Scale Data Sets. Non-parametric algorithm to identify rhythmic components in large datasets. Identifies and characterizes cycling variables in large datasets.
Proper citation: JTK_CYCLE (RRID:SCR_017962) Copy
https://www.med.upenn.edu/cbica/captk/
Software platform for analysis of radiographic cancer images. Used as quantitative imaging analytics for precision diagnostics and predictive modeling of clinical outcome.
Proper citation: Cancer Imaging Phenomics Toolkit (RRID:SCR_017323) Copy
Open Source software package for digital pathology image analysis. Used for whole slide image analysis and digital pathology. Provides researchers with batch processing and scripting functionality, and extensible platform with which to develop and share new algorithms to analyze complex tissue images.
Proper citation: QuPath (RRID:SCR_018257) Copy
https://github.com/nebneuron/neural-ideal
Software package for extracting neural activity codes.
Proper citation: Neural Ideal (RRID:SCR_017448) Copy
https://github.com/flatironinstitute/mountainsort
Neurophysiological spike sorting software.
Proper citation: MountainSort (RRID:SCR_017446) Copy
Open knowledge base that can be read and edited by both humans and machines. Storage for structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. Provides support to many other sites and services beyond just Wikimedia projects.
Proper citation: Wikidata (RRID:SCR_018492) Copy
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
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
https://chlorobox.mpimp-golm.mpg.de/geseq.html
Software tool for rapid and accurate annotation of organelle genomes, in particular chloroplast genomes.
Proper citation: GeSeq (RRID:SCR_017336) Copy
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
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
https://www.mbfbioscience.com/stereo-investigator-cleared-tissue-edition
Software tool for unbiased stereology to be used on cleared tissue. Used to analyze intact, cleared tissue specimens imaged with light sheet or confocal microscopes. Includes number, length, area and volume analyses.
Proper citation: Stereo Investigator - Cleared Tissue Edition (RRID:SCR_017668) Copy
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
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
https://ibest.github.io/HTStream/
Software tool as quality control and processing pipeline for High Throughput Sequencing data. Uses tab delimited fastq format that allows for streaming from application to application. Interoperable with other standard Linux tools., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: HTStream (RRID:SCR_018354) Copy
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
https://github.com/mitragithub/Registration
Software package to align brain slice images in atlas free manner.
Proper citation: Registration Software Mitra Lab (RRID:SCR_018353) Copy
https://github.com/lufuhao/GeneSyntenyPipeline
Software pipeline was designed to draw gene synteny plot between genomes and obtain 1 to 1 gene pairs from each genome.
Proper citation: GeneSyntenyPipeline (RRID:SCR_018198) Copy
https://github.com/ComparativeGenomicsToolkit/hal/tree/master/synteny
Software tool as conserved synteny block construction method for multiple whole-genome alignments. Implementation of DAG-based for reconstruction of synteny blocks from genome alignment.
Proper citation: halSynteny (RRID:SCR_018127) Copy
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