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https://github.com/macmanes-lab/BinPacker/blob/master/README

Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux.

Proper citation: BinPacker (RRID:SCR_017038) Copy   

•   Source: SciCrunch Registry

https://github.com/INTABiotechMJ/MITE-Tracker

Open source software tool for identifying miniature inverted repeat transposable elements in large genomes. Used to process large scale genomes, to find and classify MITEs using an efficient alignment strategy to retrieve nearby inverted repeat sequences.

Proper citation: MITE-Tracker (RRID:SCR_017030) Copy   

•   Source: SciCrunch Registry

http://barc.wi.mit.edu

Core provides consultation, training, software and educational tools in bioinformatics and graphics.

Proper citation: Whitehead Institute Bioinformatics and Research Computing Core Facility (RRID:SCR_017150) Copy   

•   Source: SciCrunch Registry

https://github.com/g2-bernotas/PS-Plant-Framework

Software tool as end to end software for data acquisition, processing, and result extraction of Arabidopsis thaliana growth. Framework uses photometric stereo based 3D imaging system with computer vision and deep learning for tracking and quantifying both plant growth and movement parameters.

Proper citation: PS-Plant Framework (RRID:SCR_017032) Copy   

•   Source: SciCrunch Registry

https://ous-research.no/bioinformatics/

Core facility provides high throughput sequencing data analysis, metagenomics data analysis, proteomics data analysis, protein structure analysis, functional genomics, programming, scripting, and database or web services.

Proper citation: Rikshospitalet-Radiumhospitalet and University of Oslo Bioinformatics Core Facility (RRID:SCR_017152) Copy   

•   Source: SciCrunch Registry

https://github.com/BDI-pathogens/phyloscanner

Software tool for analysing pathogen genetic diversity and relationships between and within hosts at once, in windows along genome. Inferring transmission from within and between host pathogen genetic diversity.

Proper citation: phyloscanner (RRID:SCR_017400) Copy   

•   Source: SciCrunch Registry

https://www.oxinst.com/

Commercial organization located in Abingdon, United Kingdom for high technology products. Manufactures instruments for agriculture, astronomy, automotive, aerospace, bio-imaging, life science, chemical and catalysis, energy generation and storage, forensics, environmental industries, geology, metallurgy, pharmacy, photonics, polymers, quantum technology, data storage, and microelectronics. Products are divided into atom force microscopy, electron microscopy, deposition and etch tools, low temperature systems, optical imaging, nuclear magnetic resonance, MRI and CT servicing, Modular optical spectroscopy, and X-Ray.

Proper citation: Oxford Instruments (RRID:SCR_017366) Copy   

•   Source: SciCrunch Registry

https://github.com/raamana/neuropredict

Software tool for assessment of predictive power, with support for neuroimaging features. Easy machine learning and standardized predictive analysis of biomarkers.

Proper citation: neuropredict (RRID:SCR_017405) Copy   

•   Source: SciCrunch Registry

https://github.com/raamana/graynet

Software tool for subject wise networks from morphometric features and structural MRI. Single subject morphometric networks for neuroscience connectivity applications.

Proper citation: graynet (RRID:SCR_017406) Copy   

•   Source: SciCrunch Registry

https://www.liebertpub.com/doi/pdf/10.1089/15279160150518540

Software package for statistical analysis by SAS Institute Inc, Cary, NC.

Proper citation: StatView Version 5.0 (RRID:SCR_017411) Copy   

•   Source: SciCrunch Registry

https://usegalaxy.eu

Software tool for analysis of mass spectrometry imaging data implemented in Galaxy framework. Provides options to analyze mass spectrometry imaging data in imzML file format, including quality control, visualization, preprocessing, statistical analysis, image co-registration and feature identification.Galaxy docker container for mass spectrometry imaging.

Proper citation: Mass spectrometry imaging workbench (RRID:SCR_017410) Copy   

•   Source: SciCrunch Registry

http://rtools.cbrc.jp/centroidfold/

Web server for RNA secondary structure prediction. Predicts RNA secondary structure from RNA sequence. Based on generalized centroid estimator.

Proper citation: CentroidFold (RRID:SCR_017253) Copy   

•   Source: SciCrunch Registry

http://www.agilemwt.com/index.htm

Manufacturer, located in Cary, North Carolina, USA, of amplifiers, RF/microwaves, and other electrical components which come in boards, modules, or systems.

Proper citation: Agile Microwave Technology Inc. (RRID:SCR_017373) Copy   

•   Source: SciCrunch Registry

http://www.bio-rad.com/en-eh/product/cfx-manager-software

Software tool to analyze real-time PCR data and run PCR system in software controlled mode., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CFX Manager (RRID:SCR_017251) Copy   

•   Source: SciCrunch Registry

https://github.com/ruanjue/wtdbg2.git

Software tool as de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. It assembles raw reads without error correction and then builds consensus from intermediate assembly output. Desiged to assemble huge genomes in very limited time.

Proper citation: WTDBG (RRID:SCR_017225) Copy   

•   Source: SciCrunch Registry

https://www.mbfbioscience.com/neuroinfo

Software for automatic identification and delineation of brain regions within experimental mouse brain sections. NeuroInfo registers serial section images of any orientation to Allen Mouse Brain Atlas, corrects for distortion due to histological processing, delineates anatomies in experimental section, and detects and reports on cell number within selected anatomies.

Proper citation: NeuroInfo (RRID:SCR_017346) Copy   

•   Source: SciCrunch Registry

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

Software R package for analysis of phylogenetics and evolution. Environment for modern phylogenetics and evolutionary analyses in R.

Proper citation: ape (RRID:SCR_017343) Copy   

•   Source: SciCrunch Registry

https://github.com/lh3/psmc.git

Software package for implementation of Pairwise Sequentially Markovian Coalescent model. Infers population size history from diploid sequence.

Proper citation: PSMC (RRID:SCR_017229) Copy   

•   Source: SciCrunch Registry

http://wasabiapp.org/software/prank/

Software application as probabilistic multiple alignment program for DNA, codon and amino-acid sequences. Allows for defining potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.

Proper citation: prank (RRID:SCR_017228) Copy   

•   Source: SciCrunch Registry

https://github.com/theaidenlab/3d-dna.git

Software tool as 3D de novo assembly (3D DNA) pipeline. Used to help generate HI-C assembly.

Proper citation: 3D de novo assembly (RRID:SCR_017227) Copy   

•   Source: SciCrunch Registry