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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Human Reference Protein Interactome Project Resource Report Resource Website 10+ mentions |
Human Reference Protein Interactome Project (RRID:SCR_015670) | HuRI | portal, project portal, web application, data or information resource, database, software resource | Project portal for the Human Reference Protein Interactome Project, which aims generate a first reference map of the human protein-protein interactome network by identifying binary protein-protein interactions (PPIs). It achieves this by systematically interrogating all pairwise combinations of predicted human protein-coding genes using proteome-scale technologies. | protein interactome, protein-protein interaction, ppi, pairwise combination, proteome, human reference | NHGRI R01/U01HG001715; NHGRI P50HG004233; NHLBI U01HL098166; NHLBI U01HL108630; NCI U54CA112962; NCI R33CA132073; NIH RC4HG006066; NICHD ARRA R01HD065288; NICHD ARRA R21MH104766; NICHD ARRA R01MH105524; NIMH R01MH091350; NSF CCF-1219007; NSERC RGPIN-2014-03892 |
PMID:25416956 | Freely Available, Free, Available for download | SCR_015670 | HuRI: The Human Reference Protein Interactome Mapping Project | 2026-08-11 09:43:11 | 20 | |||||||
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Signal Resource Report Resource Website 500+ mentions |
Signal (RRID:SCR_014276) | data analysis software, software application, data acquisition software, software resource, data processing software | A sweep-based data acquisition and analysis software package. Its uses range from a simple storage oscilloscope to complex applications requiring stimulus generation, data capture, control of external equipment and custom analysis. A built-in script language automates tasks and provides additional tools for custom analyses and applications. Signal includes functions for specific application areas, including dynamic clamp, whole cell and patch clamp electrophysiology, and evoked response including control of magnetic and other stimulus devices. Video tutorials and a demo version of Signal is available on the main page. | sweep based, data acquisition software, data analysis software, | Pay for product | SCR_014276 | 2026-08-11 09:42:44 | 737 | |||||||||||
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Psykinematix Resource Report Resource Website 10+ mentions |
Psykinematix (RRID:SCR_014830) | data analysis software, software application, standalone software, data acquisition software, software resource, data processing software | Standalone solution dedicated to Visual Psychophysics running on Mac OS X. Psykinematix runs standard psychophysical protocols, presents complex stimuli, collects subject's responses, and analyzes results on the fly. It consists of a unique OpenGL-based software package that does not require any programming skill to create and run complex experiments. | psychophysics, visual psychophysics, standalone, mac, data analysis, data acquisition, experiment | Demo is available, Available for download, License required | SCR_014830 | 2026-08-11 09:42:56 | 21 | |||||||||||
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National Institute on Drug Abuse Center for Genetic Studies Resource Report Resource Website 1+ mentions |
National Institute on Drug Abuse Center for Genetic Studies (RRID:SCR_013061) | NIDA Center for Genetic Studies | service resource, data or information resource, storage service resource, data set, data repository | Site for collection and distribution of clinical data related to genetic analysis of drug abuse phenotypes. Anonymous data on family structure, age, sex, clinical status, and diagnosis, DNA samples and cell line cultures, and data derived from genotyping and other genetic analyses of these clinical data and biomaterials, are distributed to qualified researchers studying genetics of mental disorders and other complex diseases at recognized biomedical research facilities. Phenotypic and Genetic data will be made available to general public on release dates through distribution mechanisms specified on website. | drug abuse, family, family structure, genetic analysis, genetics, addiction, age, biomaterial, cell line, citation, clinical, clinical status, data, diagnosis, dna, genotyping, human, mental disorder, mutation analysis, phenotype, publications, sex, clinical data, genotype, gene, GWAS |
is recommended by: National Library of Medicine is listed by: One Mind Biospecimen Bank Listing is related to: One Mind Biospecimen Bank Listing is related to: NIH Data Sharing Repositories has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA has parent organization: Rutgers University; New Jersey; USA |
NIDA ; NIH Blueprint for Neuroscience Research |
Free, Freely available | nif-0000-00181 | https://zork5.wustl.edu//nida/ | http://zork.wustl.edu/nida/ | SCR_013061 | National Institute of Drug Abuse (NIDA) Human Genetics Initiative, NIDA Center for Genetic Studies | 2026-08-11 09:42:32 | 7 | ||||
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NIH-CIDI Lung Segmentation Tool Resource Report Resource Website 1+ mentions |
NIH-CIDI Lung Segmentation Tool (RRID:SCR_014150) | software application, image analysis software, software resource, segmentation software, data processing software | 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 | CIDI-lung-seg, CIDI Lung Seg | 2026-08-11 09:42:43 | 1 | ||||||||
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ImmunoStar Resource Report Resource Website 500+ mentions |
ImmunoStar (RRID:SCR_013473) | antibody supplier, reagent supplier, commercial organization, material resource | An Antibody supplier | nlx_152388 | SCR_013473 | Immunonuclear, Diasorin, Incstar, Immuno Nuclear, ImmunoStar inc. | 2026-08-11 09:42:36 | 661 | |||||||||||
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xFITOM Resource Report Resource Website 1+ mentions |
xFITOM (RRID:SCR_014445) | data analysis software, software application, standalone software, software resource, data processing software, sequence analysis 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 | 2026-08-11 09:42:49 | 7 | |||||||
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PLINK/SEQ Resource Report Resource Website 50+ mentions |
PLINK/SEQ (RRID:SCR_013193) | software toolkit, software application, software resource, software library | 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 | 2026-08-11 09:42:42 | 77 | ||||||||
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LeafCutter Resource Report Resource Website 10+ mentions |
LeafCutter (RRID:SCR_017639) | data analysis software, software application, software resource, data processing software, data analytics software | 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 | 2026-08-11 09:43:32 | 32 | ||||||||
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HiC-Pro Resource Report Resource Website 100+ mentions |
HiC-Pro (RRID:SCR_017643) | software application, workflow software, data processing software, software resource | 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 |
France Genomique National infrastructure ; Labex Deep ; European Research Coucil ; ERC Advanced Investigator award ; European Commission ; ABS4NGS project ; National Human Genome Research Institute ; Paris Alliance of Cancer Research Institutes ; Howard Hughes Medical Institute |
PMID:26619908 | Free, Available for download, Freely available | biotools:hic-pro | https://bio.tools/hic-pro | SCR_017643 | 2026-08-11 09:43:39 | 238 | ||||||
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Thunder Resource Report Resource Website 10+ mentions |
Thunder (RRID:SCR_016556) | data analysis software, software application, image analysis software, software resource, data processing software | 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 | 2026-08-11 09:43:21 | 10 | |||||||||||
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cgpPindel Resource Report Resource Website 10+ mentions |
cgpPindel (RRID:SCR_017090) | data analysis software, data processing software, software resource, software application | 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 | 2026-08-11 09:43:36 | 26 | ||||||||||
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tenx Resource Report Resource Website 10+ mentions |
tenx (RRID:SCR_016957) | service resource, analysis service resource, software toolkit, software resource, data analysis service, production service resource | 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 | 2026-08-11 09:43:27 | 13 | |||||||||||
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Mizutani Lab 3D Structure Portal Resource Report Resource Website 1+ mentions |
Mizutani Lab 3D Structure Portal (RRID:SCR_016529) | portal, service resource, data or information resource, storage service resource, organization portal, data repository, laboratory portal | 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 | 2026-08-11 09:43:19 | 2 | |||||||||||
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Marvel Resource Report Resource Website 1+ mentions |
Marvel (RRID:SCR_017621) | software application, alignment software, software toolkit, image analysis software, software resource, data processing software | 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 | 2026-08-11 09:43:39 | 2 | |||||||||||
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Letswave Resource Report Resource Website 10+ mentions |
Letswave (RRID:SCR_016414) | software application, software toolkit, software resource, data processing software, data visualization software | 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 | 2026-08-11 09:43:18 | 27 | |||||||||
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TSDiffAna Resource Report Resource Website 1+ mentions |
TSDiffAna (RRID:SCR_016656) | data analysis software, software application, image analysis software, software resource, data processing software | 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 | 2026-08-11 09:43:21 | 2 | |||||||||
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Nutil - Neuroimaging utilities Resource Report Resource Website 10+ mentions |
Nutil - Neuroimaging utilities (RRID:SCR_017183) | Nutil | software application, software toolkit, image analysis software, image processing software, software resource, data processing software | 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 | Neuroimaging utilities | 2026-08-11 09:43:31 | 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 | portal, service resource, topical portal, data or information resource, storage service resource, database, disease-related portal, organization portal, data repository | 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 | the Common Fund’s Gabriella Miller Kids First Pediatric Research Program ; NIH |
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 | Data Resource Portal | 2026-08-11 09:43:25 | 6 | ||||
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Computer Vision System Toolbox Resource Report Resource Website 1+ mentions |
Computer Vision System Toolbox (RRID:SCR_017581) | software application, software toolkit, image processing software, software resource, data processing software | 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 | Computer Vision Toolbox, MATLAB Computer Vision System Toolbox | 2026-08-11 09:43:38 | 4 |
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