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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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NIH-CIDI Lung Segmentation Tool Resource Report Resource Website 1+ mentions |
NIH-CIDI Lung Segmentation Tool (RRID:SCR_014150) | data processing software, image analysis software, segmentation software, software application, software resource | A segmentation tool for the segmentation of a lung from CT images. The sofware can be run in two modes: fully automatic and semi-automatic with manual seeding by the user. The software also allows the user to perform basic filtering operations and manual correction to the segmentation. The VTK-based rendering implementation, along with option to view in axial, coronal, and sagittal, provides the user with better visualization of the segmented lung. | segmentation software, lung, ct image, visualization |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: National Institutes of Health |
PMID:25570151 | Open source | SCR_014150 | SciCrunch Registry | CIDI-lung-seg, CIDI Lung Seg | 2026-10-10 12:41:51 | 1 | ||||||||
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ImmunoStar Resource Report Resource Website 500+ mentions |
ImmunoStar (RRID:SCR_013473) | antibody supplier, commercial organization, material resource, reagent supplier | An Antibody supplier | nlx_152388 | SCR_013473 | SciCrunch Registry | Immunonuclear, Diasorin, Incstar, Immuno Nuclear, ImmunoStar inc. | 2026-10-10 12:41:49 | 661 | |||||||||||
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xFITOM Resource Report Resource Website 1+ mentions |
xFITOM (RRID:SCR_014445) | data analysis software, data processing software, sequence analysis software, software application, software resource, standalone software | A fully customizable program that uses a graphical user interface to locate transcription factor-binding sites in genomic sequences. xFITOM scans DNA or RNA sequences for putative binding sites as defined by a collection of aligned known sites, a consensus sequence in IUPAC degenerate-base format, or a combination of the two. | transcription factor, binding site, information theory, customizable program, sequence analysis software |
uses: GenBank is related to: CollecTF |
PMID:21346861 | Available for download, Acknowledgement requested | http://www.mybiosoftware.com/fitom-1-0-detection-binding-sites-dna-rna-sequences.html | compbio.umbc.edu/Software/xFITOM/ http://research.umbc.edu/~erill/ | SCR_014445 | SciCrunch Registry | 2026-10-10 12:41:51 | 7 | |||||||
|
PLINK/SEQ Resource Report Resource Website 50+ mentions |
PLINK/SEQ (RRID:SCR_013193) | software application, software library, software resource, software toolkit | An open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing projects, particularly whole-exome and whole-genome studies. However, the library could in principle be applied to other types of genetic studies, including whole-genome association studies of common SNPs. (entry from Genetic Analysis Software) | gene, genetic, genomic, c/c++, r, macos, linux, bio.tools |
is listed by: Genetic Analysis Software is listed by: bio.tools is listed by: Debian is related to: PLINK has parent organization: Harvard University; Cambridge; United States |
Open unspecified license | nlx_154213, biotools:plink-seq | https://bio.tools/plink-seq | SCR_013193 | SciCrunch Registry | 2026-10-10 12:41:46 | 77 | ||||||||
|
LeafCutter Resource Report Resource Website 10+ mentions |
LeafCutter (RRID:SCR_017639) | data analysis software, data analytics software, data processing software, software application, software resource | Software tool for identifying and quantifying RNA splicing variation. Used to study sample and population variation in intron splicing. Identifies variable intron splicing events from short read RNA-seq data and finds alternative splicing events of high complexity. Used for detecting differential splicing between sample groups, and for mapping splicing quantitative trait loci (sQTLs). | Identify, quantitate, RNA, splicing, variation, intron, short, read, RNAseq, data, mapping, trait, loci, sQTL | has parent organization: Stanford University; Stanford; California | CEHG Fellowship ; Howard Hughes Medical Institute ; NHGRI HG007036; NHGRI HG008140; NHGRI HG009431; NIMH R01 MH107666 |
PMID:29229983 DOI:10.1038/s41588-017-0004-9 |
Free, Available for download, Freely available | SCR_017639 | SciCrunch Registry | 2026-10-10 12:41:50 | 32 | ||||||||
|
HiC-Pro Resource Report Resource Website 100+ mentions |
HiC-Pro (RRID:SCR_017643) | data processing software, software application, software resource, workflow software | Software tool as optimized and flexible pipeline for Hi-C data processing. Used to process Hi-C data, from raw fastq files, paired end Illumina data, to normalized contact maps. | Hi-C, data, raw, fastq, file, paired, Illumina, normalized, contact, map, bio.tools |
is listed by: Debian is listed by: bio.tools |
ABS4NGS project ; ERC Advanced Investigator award ; European Commission ; European Research Coucil ; France Genomique National infrastructure ; Howard Hughes Medical Institute ; Labex Deep ; National Human Genome Research Institute ; Paris Alliance of Cancer Research Institutes |
PMID:26619908 | Free, Available for download, Freely available | biotools:hic-pro | https://bio.tools/hic-pro | SCR_017643 | SciCrunch Registry | 2026-10-10 12:41:56 | 238 | ||||||
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Thunder Resource Report Resource Website 10+ mentions |
Thunder (RRID:SCR_016556) | data analysis software, data processing software, image analysis software, software application, software resource | 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. | Free, Available for download, Freely available, Tutorial available | https://github.com/thunder-project/thunder | SCR_016556 | SciCrunch Registry | 2026-10-10 12:41:48 | 10 | |||||||||||
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cgpPindel Resource Report Resource Website 10+ mentions |
cgpPindel (RRID:SCR_017090) | data analysis software, data processing software, software application, software resource | Software tool as cancer genome project insertion or deletion detection workflow for Pindel. | works with: Pindel | Free, Available for download, Freely available | http://cancerit.github.io/cgpPindel/ | SCR_017090 | SciCrunch Registry | 2026-10-10 12:41:49 | 26 | ||||||||||
|
tenx Resource Report Resource Website 10+ mentions |
tenx (RRID:SCR_016957) | analysis service resource, data analysis service, production service resource, service resource, software resource, software toolkit | 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. | analysis, 10x, single, cell, RNA, sequencing, data, genomic, platform, mapping, quantitation | Free, Available for download, Freely available | SCR_016957 | SciCrunch Registry | 2026-10-10 12:41:49 | 13 | |||||||||||
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Mizutani Lab 3D Structure Portal Resource Report Resource Website 1+ mentions |
Mizutani Lab 3D Structure Portal (RRID:SCR_016529) | data or information resource, data repository, laboratory portal, organization portal, portal, service resource, storage service resource | 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. | computed, tomography, visualize, 3D structure, biological, soft, tissue, imaging, sectioning, | Free, Available for download, Freely available, DVDs commercially available | SCR_016529 | SciCrunch Registry | 2026-10-10 12:41:53 | 2 | |||||||||||
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Marvel Resource Report Resource Website 1+ mentions |
Marvel (RRID:SCR_017621) | alignment software, data processing software, image analysis software, software application, software resource, software toolkit | Software set of tools that facilitate overlapping, patching, correction and assembly of noisy long reads. | Overlapping, patching, correction, assembly, noisy, long, read, sequence, align | Free, Available for download, Freely available | SCR_017621 | SciCrunch Registry | 2026-10-10 12:41:54 | 2 | |||||||||||
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Letswave Resource Report Resource Website 10+ mentions |
Letswave (RRID:SCR_016414) | data processing software, data visualization software, software application, software resource, software toolkit | Open source electroencephalogram (EEG) signal processing toolbox to process and visualise EEG/MEG data and other neurophysiological signals. | process, visualise, EEG, MEG, data, neurophysiological, signal, brain, neuroscience | is related to: MATLAB | Free, Available for download, Freely available | https://www.letswave.org/ | SCR_016414 | SciCrunch Registry | 2026-10-10 12:41:53 | 27 | |||||||||
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TSDiffAna Resource Report Resource Website 1+ mentions |
TSDiffAna (RRID:SCR_016656) | data analysis software, data processing software, image analysis software, software application, software resource | 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. | SPM, statistical, parametiric, mapping, slicewise, scan, difference, standard, deviation, quality, image, neuroimaging, data |
has parent organization: University College London; London; United Kingdom is provided by: SPM |
Free, Available for download, Freely available | https://sourceforge.net/projects/tsdiffana.spmtools.p/ | SCR_016656 | SciCrunch Registry | 2026-10-10 12:41:49 | 2 | |||||||||
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DoG picker Resource Report Resource Website 10+ mentions |
DoG picker (RRID:SCR_016655) | DoG picker | data processing software, image processing software, software application, software resource | 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. | general, single, particle, picking, macromolecule, size, selection, electron, microscopy, image, transform | is listed by: OMICtools | NCRR RR17573; NCRR RR23093 |
PMID:19374019 | THIS RESOURCE IS NO LONGER IN SERVICE | http://emg.nysbc.org/redmine/projects/appion/wiki/Appion_Home | SCR_016655 | SciCrunch Registry | Difference of Gaussians (DoG) picker, Difference of Gaussians Picker, Difference of Gaussians picker | 2026-10-10 12:42:19 | 23 | |||||
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Nutil - Neuroimaging utilities Resource Report Resource Website 10+ mentions |
Nutil - Neuroimaging utilities (RRID:SCR_017183) | Nutil | data processing software, image analysis software, image processing software, software application, software resource, software toolkit | 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. | neuroscience, 2D, brain, image, data, processing, analysis |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Allen Institute for Brain Science has parent organization: University of Oslo; Oslo; Norway works with: VisuAlign |
European Union’s Horizon 2020 Framework Programme for Research and Innovation under the Framework Partnership Agreement No. 650003 (HBP FPA) and the European Union’s Horizon Europe Programme for Research Infrastructures Grant Agreement No. 101147319 (EBRAINS 2.0). | PMID:32973479 | Free, Available for download, Freely available | https://nutil.readthedocs.io; https://github.com/Neural-Systems-at-UIO/nutil | SCR_017183 | SciCrunch Registry | Neuroimaging utilities | 2026-10-10 12:41:55 | 28 | |||||
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Kids First Data Resource Portal Resource Report Resource Website 1+ mentions |
Kids First Data Resource Portal (RRID:SCR_016493) | DRP | data or information resource, data repository, database, disease-related portal, organization portal, portal, service resource, storage service resource, topical portal | 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. | pediatric, genomic, clinical, disease, data, children, cancer, birth, defect, analysis | is recommended by: National Library of Medicine | pediatric cancer, birth defect | NIH ; the Common Fund’s Gabriella Miller Kids First Pediatric Research Program |
Restricted | SCR_016553 | https://commonfund.nih.gov/kidsfirst, https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs001168.v1.p1, https://commonfund.nih.gov/kidsfirst | SCR_016493 | SciCrunch Registry | Data Resource Portal | 2026-10-10 12:41:53 | 6 | ||||
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Computer Vision System Toolbox Resource Report Resource Website 1+ mentions |
Computer Vision System Toolbox (RRID:SCR_017581) | data processing software, image processing software, software application, software resource, software toolkit | 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. | The MathWorks, Inc. designing, testing, computer, vision, 3D, video, processing, system, MATLAB, object, detection, tracking | is related to: MATLAB | Restricted | SCR_017581 | SciCrunch Registry | Computer Vision Toolbox, MATLAB Computer Vision System Toolbox | 2026-10-10 12:41:49 | 4 | |||||||||
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numerical-fitting Resource Report Resource Website |
numerical-fitting (RRID:SCR_016025) | software library, software resource, software toolkit | Software for a numerical computation library that performs numerical calculations. Used in ABCD study. | numerical, computation, library, calculation, performing, client, side, javascript, js, abcd |
is related to: University of California at San Diego; California; USA works with: ABCD Study |
NIDA U24 DA041123 | Free, Available for download | SCR_016025 | SciCrunch Registry | 2026-10-10 12:41:52 | 0 | |||||||||
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OrthoFinder Resource Report Resource Website 1000+ mentions |
OrthoFinder (RRID:SCR_017118) | data analysis software, data processing software, software application, software resource | 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. | comparative, genomic, analysis, find, orthogroup, ortholog, infer, gene, tree, duplicate, accuracy, protein, sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Bill and Melinda Gates Foundation ; UKAID |
PMID:26243257 DOI:10.1101/466201 |
Free, Available for download, Freely available | biotools:OrthoFinder, OMICS_09733, BioTools:OrthoFinder | https://bio.tools/OrthoFinder, https://bio.tools/OrthoFinder, https://bio.tools/OrthoFinder | SCR_017118 | SciCrunch Registry | OrthoFinder2, OrthoFinder | 2026-10-10 12:41:53 | 3413 | |||||
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Phaff Yeast Culture Collection Resource Report Resource Website 1+ mentions |
Phaff Yeast Culture Collection (RRID:SCR_016781) | data or information resource, database, organization portal, portal, service resource | 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. | yeast, strain, wild, screening, selection, service | has parent organization: University of California at Davis; California; USA | Commercially available | SCR_016781 | SciCrunch Registry | 2026-10-10 12:42:19 | 6 |
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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant U24DK097771.
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