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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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Leica: LMD7 Laser Microdissection microscope Resource Report Resource Website 1+ mentions |
Leica: LMD7 Laser Microdissection microscope (RRID:SCR_024657) | instrument resource | Laser Microdissection system enables users to isolate specific single cells or entire areas of tissue. Powered by unique laser design and dynamic software, Leica LMD systems allow users to easily isolate Regions of Interest from entire areas of tissue down to single cells or even subcellular structures such as chromosomes. LMD7 provides higher laser power. Suited to dissect any kind of tissue independent of its size or shape. | Laser Microdissection system, microscope, Leica, isolate specific single cells, isolate entire areas of tissue, dissect any kind of tissue, tissue independent of its size or shape, | https://drive.google.com/file/d/1GYFvceHIJyw9ybdYC9r2YThVHlKKHcQU/view?usp=sharing | Model_Number_LMD7 | https://manualzz.com/doc/17928252/leica_lmd6_7-technicalbrochure_en_2016.03.24 | SCR_024657 | Leica LMD7 | 2026-08-29 11:28:36 | 1 | ||||||||
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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 | 2026-08-29 11:28:12 | 32 | ||||||||
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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 | 2026-08-29 11:27:45 | 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 | 2026-08-29 11:28:08 | 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 | 2026-08-29 11:27:43 | 26 | ||||||||||
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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 | 2026-08-29 11:27:43 | 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 | 2026-08-29 11:27:41 | 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 | 2026-08-29 11:28:11 | 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 | 2026-08-29 11:28:08 | 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 | 2026-08-29 11:27:41 | 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 | Difference of Gaussians (DoG) picker, Difference of Gaussians Picker, Difference of Gaussians picker | 2026-08-29 11:28:09 | 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 | Neuroimaging utilities | 2026-08-29 11:27:44 | 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 | Data Resource Portal | 2026-08-29 11:28:08 | 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 | Computer Vision Toolbox, MATLAB Computer Vision System Toolbox | 2026-08-29 11:27:42 | 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 | 2026-08-29 11:27:39 | 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 | OrthoFinder2, OrthoFinder | 2026-08-29 11:28:10 | 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 | 2026-08-29 11:28:09 | 6 | ||||||||||
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tximport Resource Report Resource Website 100+ mentions |
tximport (RRID:SCR_016752) | data analysis software, data processing software, software application, software resource | 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. | pseudoaligned, reads, R, differential, expression, analysis, gene, transcript, bio.tools |
is listed by: Bioconductor is listed by: Debian is listed by: bio.tools works with: edgeR works with: DESeq2 |
European Commission ; NCI T32 CA009337; SNSF 143883 |
DOI:10.12688/f1000research.7563.1 | Free, Available for download, Freely available | biotools:tximport | https://bioconductor.org/packages/tximport/, https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html, https://github.com/F1000Research/tximport, https://bio.tools/tximport | https://zenodo.org/record/35123#.W_w3behKiM8 | SCR_016752 | tximport v1.4.0 | 2026-08-29 11:27:41 | 100 | ||||
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Nephele Resource Report Resource Website 10+ mentions |
Nephele (RRID:SCR_016595) | analysis service resource, data analysis service, production service resource, service resource, software resource, web application | Cloud based platform for simplified, standardized and reproducible microbiome data analysis. Allows users to process microbiome datasets through pipelines of existing software tools. | microbiome, datasets, process, analyze, metagenome, sequencing, data, bio.tools |
uses: mothur uses: QIIME uses: biobakery uses: A5-miseq is listed by: NIAID is listed by: bio.tools is listed by: Debian has parent organization: OCICB |
NIH Department of Health and Human Services GS35F0373X | PMID:29028892 | Free, Available for download, Freely available | biotools:nephele | https://github.com/niaid/Nephele, https://bio.tools/nephele | SCR_016595 | 2026-08-29 11:27:41 | 36 | ||||||
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Cyflogic Resource Report Resource Website 10+ mentions |
Cyflogic (RRID:SCR_016635) | data analysis software, data processing software, software application, software resource, software toolkit | 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. | flow, cytometry, data, analysis, CyFlo Ltd., dot, plot, histogram, statistics | PMID:23839300 | Commercially available, Free for non-commercial research use only and not for use in diagnostic or therapeutic procedures | SCR_016635 | 2026-08-29 11:27:42 | 27 |
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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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