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http://thunder-project.org/

Software package for the analysis of image and time series data in Python. Provides data structures and algorithms for loading, processing, and analyzing these data. Runs locally or against a Spark cluster with an identical API.

Proper citation: Thunder (RRID:SCR_016556) Copy   

•   Source: SciCrunch Registry

https://github.com/cancerit/cgpPindel

Software tool as cancer genome project insertion or deletion detection workflow for Pindel.

Proper citation: cgpPindel (RRID:SCR_017090) Copy   

•   Source: SciCrunch Registry

https://github.com/sansomlab/tenx

Pipeline for the analysis of 10x single cell RNA sequencing data. Collection of python3 pipelines and Rscripts to analyze data generated with the 10x Genomics platform. The pipelines are based on 10x's Cell Ranger pipeline for mapping and quantitation and the R Seurat package for downstream analysis.

Proper citation: tenx (RRID:SCR_016957) Copy   

•   Source: SciCrunch Registry

https://mizutanilab.github.io/db.htm

Departamental portal of Applied Biochemistry, School of Engineering, Tokai University, Japan. Used for computed tomography (CT) and visualizing 3D structures of biological soft tissues represented with Cartesian coordinates.

Proper citation: Mizutani Lab 3D Structure Portal (RRID:SCR_016529) Copy   

•   Source: SciCrunch Registry

https://github.com/schloi/MARVEL

Software set of tools that facilitate overlapping, patching, correction and assembly of noisy long reads.

Proper citation: Marvel (RRID:SCR_017621) Copy   

•   Source: SciCrunch Registry

https://github.com/NOCIONS/letswave6/wiki/Download-and-setup

Open source electroencephalogram (EEG) signal processing toolbox to process and visualise EEG/MEG data and other neurophysiological signals.

Proper citation: Letswave (RRID:SCR_016414) Copy   

•   Source: SciCrunch Registry

https://www.fil.ion.ucl.ac.uk/spm/ext/#TSDiffAna

Software tool developed for Statistical Parametric Mapping (SPM) that computes slicewise scan by scan difference and standard deviations. Used to examine quality of image timeseries.

Proper citation: TSDiffAna (RRID:SCR_016656) Copy   

•   Source: SciCrunch Registry

https://omictools.com/dog-picker-tool

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18,2023. Software tool for general particle picking in the single-particle processing of unknown macromolecules. Reference free particle picker with ability to sort particles based on size or it can be used to bootstrap the creation of templates or training datasets for other particle pickers. Used to facilitate particle selection in single particle electron microscopy., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: DoG picker (RRID:SCR_016655) Copy   

•   Source: SciCrunch Registry

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

Software toolbox to simplify and streamline mechanism of pre and post processing 2D brain image data. Neuroscience image processing and analysis utilities. Stand alone application that runs on all operating systems. Nutil is part of the QUINT workflow.

Proper citation: Nutil - Neuroimaging utilities (RRID:SCR_017183) Copy   

•   Source: SciCrunch Registry

https://kidsfirstdrc.org/portal/portal-features/

Portal for analysis and interpretation of pediatric genomic and clinical data to advance personalized medicine for detection, therapy, and management of childhood cancer and structural birth defects. For patients, researchers, and clinicians to create centralized database of well curated clinical and genetic sequence data from patients with childhood cancer or structural birth defects.

Proper citation: Kids First Data Resource Portal (RRID:SCR_016493) Copy   

•   Source: SciCrunch Registry

https://www.mathworks.com/products/computer-vision.html

Software tool to provide algorithms, functions, and apps for designing and testing computer vision, 3D vision, and video processing systems for MATLAB. You can perform object detection and tracking, as well as feature detection, extraction, and matching. For 3D vision, toolbox supports single, stereo, and fisheye camera calibration; stereo vision; 3D reconstruction; and lidar and 3D point cloud processing. Computer vision apps automate ground truth labeling and camera calibration workflows.

Proper citation: Computer Vision System Toolbox (RRID:SCR_017581) Copy   

•   Source: SciCrunch Registry

https://github.com/davidemms/OrthoFinder

Software Python application for comparative genomics analysis. Finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of gene duplcation events in those gene trees, infers rooted species tree for species being analysed and maps gene duplication events from gene trees to branches in species tree, improves orthogroup inference accuracy. Runs set of protein sequence files, one per species, in FASTA format.

Proper citation: OrthoFinder (RRID:SCR_017118) Copy   

•   Source: SciCrunch Registry

http://phaffcollection.ucdavis.edu/

Collection of wild yeast in the world. Academic and industrial resarchers utilize this collection for a variety of research and applications, including pigments, enzymes, food ingredients, and hosts for protein expression. Provides contract screening and strain selection services.

Proper citation: Phaff Yeast Culture Collection (RRID:SCR_016781) Copy   

•   Source: SciCrunch Registry

https://github.com/mikelove/tximport

Software R package for importing pseudoaligned reads into R for use with downstream differential expression analysis. Used for import and summarize transcript level estimates for transcript and gene level analysis.

Proper citation: tximport (RRID:SCR_016752) Copy   

•   Source: SciCrunch Registry

https://nephele.niaid.nih.gov

Cloud based platform for simplified, standardized and reproducible microbiome data analysis. Allows users to process microbiome datasets through pipelines of existing software tools.

Proper citation: Nephele (RRID:SCR_016595) Copy   

•   Source: SciCrunch Registry

http://www.diabetes-translation.org

Centers that are part of an integrated program whose cores support and enhance diabetes type II translation research. The CDTRs aim to enhance the efficiency, productivity, effectiveness and multidisciplinary nature of diabetes translation research.

Proper citation: Centers for Diabetes Translation Research (RRID:SCR_015149) Copy   

•   Source: SciCrunch Registry

http://www.cyflogic.com/

Software tool for a flow cytometry data analysis for Microsoft Windows enviroment developed by CyFlo Ltd. Has analysis capabilities, such as dot plot, histogram and statistics.

Proper citation: Cyflogic (RRID:SCR_016635) Copy   

•   Source: SciCrunch Registry

https://sciex.com/products/software/analyst-tf-software

Acquisition software for mass spectrometry data from TripleTOF instrument(s). Analyst provides functionality for instrument control, data analysis, reporting, and audit trail.

Proper citation: Analyst®TF Software (RRID:SCR_015785) Copy   

•   Source: SciCrunch Registry

http://pixelink.com/home/products/software/drivers/

Software application for real-time, interactive, multi-camera recording. It is compatible with all Pixelink PL-B and PL-D line of cameras.

Proper citation: Pixelink Image Capture Software (RRID:SCR_016197) Copy   

•   Source: SciCrunch Registry

https://cgb.indiana.edu

CGB offers range of genomic services, including high-throughput DNA/RNA extraction, library preparation, next-generation sequencing, and bioinformatic analysis.

Proper citation: Indiana University Center for Genomics and Bioinformatics Core Facility (RRID:SCR_017165) Copy   

•   Source: SciCrunch Registry