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https://github.com/brain-life/encode

Software that implements a framework to encode structural brain connectomes into multidimensional arrays (tensors). Encoding Connectomes provides an agile framework for computing over connectome edges and nodes.

Proper citation: Linear Fascicle Evaluation (RRID:SCR_016153) Copy   

•   Source: SciCrunch Registry
  

http://www2.mrc-lmb.cam.ac.uk/relion

Software for determination of cryo-EM structures. It employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy.

Proper citation: RELION (RRID:SCR_016274) Copy   

•   Source: SciCrunch Registry
  

https://hirnetwork.org/project/hirncc

Consortium that provides infrastructure to promote communication and collaboration among current and future HIRN participants, facilitating scientific advances and the sharing of data, tools, and reagents among HIRN members and the research community at large.

Proper citation: HIRN Coordinating Center (RRID:SCR_016395) Copy   

•   Source: SciCrunch Registry
  

https://github.com/CAMI-challenge/AMBER

Software toolkit for the comparative assessment of genome reconstructions from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects.

Proper citation: AMBER (RRID:SCR_016151) Copy   

•   Source: SciCrunch Registry
  

http://vensim.com/

Simulation software for improving the performance of real systems. Used for developing, analyzing, and packaging dynamic feedback models.

Proper citation: Vensim (RRID:SCR_016394) Copy   

•   Source: SciCrunch Registry
  

https://nemoarchive.org/

Data repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification, histone modification profiles and chromatin accessibility.

Proper citation: NeMOarchive (RRID:SCR_016152) Copy   

•   Source: SciCrunch Registry
  

https://ccrod.cancer.gov/confluence/display/ROB2/Home

Software that performs quantitative analysis of angiogenesis. It specializes in quantitative assessment of various vessel morphometric and spatial parameters, including vessel length and density, branching index, lacunarity, etc.

Proper citation: AngioTool (RRID:SCR_016393) Copy   

•   Source: SciCrunch Registry
  

http://zzlab.net/blink/index.html

Software for next level of genome wide association studies with both individuals and markers in millions. The method releases the requirement that causative genes are evenly distributed on genome and consequently boosts statistical power.

Proper citation: BLINK (RRID:SCR_016288) Copy   

•   Source: SciCrunch Registry
  

https://github.com/nighres/nighres

Software package for processing of high-resolution neuroimaging data. Nighres is a community-developed project that aims to make neuroscience data tools easier to install, use and extend.

Proper citation: Nighres (RRID:SCR_016287) Copy   

•   Source: SciCrunch Registry
  

http://www.nitrc.org/projects/longhippsegm/

Software based on robust registration and simultaneous hippocampal segmentation and longitudinal marker classification of brain MRI of an arbitrary number of time points. The framework comprises two parts: a longitudinal segmentation and a longitudinal classification step.

Proper citation: Longitudinal neuroimaging hippocampal markers for diagnosing Alzheimer's disease (RRID:SCR_016282) Copy   

•   Source: SciCrunch Registry
  

https://huttenhower.sph.harvard.edu/humann2

Software for profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data Used for millions of short DNA/RNA reads. This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members.

Proper citation: HUMAnN2 (RRID:SCR_016280) Copy   

•   Source: SciCrunch Registry
  

https://github.com/jbelyeu/SV-plaudit

Software for rapidly curating structural variant (SVs) predictions. SV-plaudit provides a pipeline for creating image views of genomic intervals, automatically storing them in the cloud, deploying a website to view/score them, and retrieving scores for analysis.

Proper citation: SV-plaudit (RRID:SCR_016285) Copy   

•   Source: SciCrunch Registry
  

http://hyphy.org/

Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning.

Proper citation: HyPhy (RRID:SCR_016162) Copy   

•   Source: SciCrunch Registry
  

https://sites.google.com/site/sigenproject/

Software to extract and trace neuronal structure from confocal laser scanning microscope images. It performs the automatic reconstruction of neurons for image stacks and can generate compartmental models of neurons as swc file format data.

Proper citation: SIGEN (RRID:SCR_016284) Copy   

•   Source: SciCrunch Registry
  

http://abacus.gene.ucl.ac.uk/software/indelible/

Software that generates nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. It is used for biological sequence simulation of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time.

Proper citation: Indelible (RRID:SCR_016163) Copy   

•   Source: SciCrunch Registry
  

https://bitbucket.org/mugqic/genpipes/src/master/

Software for genomics and bioinformatics analysis. GenPipes includes several python pipelines that cover many genomics applications, such as RNASeq, ChIPSeq, DNASeq, WGBS, HiC, Metagenomics, PacBio assembly, etc.

Proper citation: GenPipes (RRID:SCR_016376) Copy   

•   Source: SciCrunch Registry
  

https://www.genomics.agilent.com/article.jsp?pageId=2100

Software that performs data analysis algorithms for QPCR data. The software is included with the purchase of the Agilent MxPro QPCR System., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MxPro QPCR (RRID:SCR_016375) Copy   

•   Source: SciCrunch Registry
  

https://github.com/sdparekh/zUMIs

Software pipeline to process RNA-seq data with UMIs. The input to this pipeline is paired-end fastq files, where one read contains the cDNA sequence and the other read contains UMI and Cell Barcode information.

Proper citation: zUMIs (RRID:SCR_016139) Copy   

•   Source: SciCrunch Registry
  

https://www.microsoft.com/en-gb/

Software application with data analysis tools and spreadsheet templates to track and visualize data. It is used to manage and process data.

Proper citation: Microsoft Excel (RRID:SCR_016137) Copy   

•   Source: SciCrunch Registry
  

https://sanger-pathogens.github.io/gubbins/

Software application as an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. It is used for phylogenetic analysis of genome sequences and generating highly accurate reconstructions under realistic models of short-term bacterial evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Gubbins (RRID:SCR_016131) Copy   

•   Source: SciCrunch Registry