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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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PLINK/SEQ Resource Report Resource Website 50+ mentions |
PLINK/SEQ (RRID:SCR_013193) | software library, software application, software toolkit, software resource | 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 | 2026-08-12 10:50:45 | 77 | ||||||||
|
LeafCutter Resource Report Resource Website 10+ mentions |
LeafCutter (RRID:SCR_017639) | software application, data processing software, data analytics software, software resource, data analysis 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 | 2026-08-12 10:51:52 | 32 | ||||||||
|
HiC-Pro Resource Report Resource Website 100+ mentions |
HiC-Pro (RRID:SCR_017643) | data processing software, workflow software, software resource, software application | 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 | 2026-08-12 10:51:51 | 238 | ||||||
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Thunder Resource Report Resource Website 10+ mentions |
Thunder (RRID:SCR_016556) | image analysis software, software application, data processing software, software resource, data analysis 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 | 2026-08-12 10:51:35 | 10 | |||||||||||
|
emmeans Resource Report Resource Website 100+ mentions |
emmeans (RRID:SCR_018734) | software application, data processing software, data analytics software, software resource, data analysis software | Software R package to obtain estimated marginal means for linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and other displays. | Estimated marginal mean, liner model, mixed model, obtain estimated marginal mean, EMMs, linear function, slope comparison, plot | is related to: CRAN | Free, Available for download, Freely available | https://github.com/rvlenth/emmeans | SCR_018734 | Least Squares Means, Estimated Marginal Means | 2026-08-12 10:52:12 | 195 | ||||||||
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cgpPindel Resource Report Resource Website 10+ mentions |
cgpPindel (RRID:SCR_017090) | data processing software, data analysis 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 | 2026-08-12 10:51:36 | 26 | ||||||||||
|
tenx Resource Report Resource Website 10+ mentions |
tenx (RRID:SCR_016957) | service resource, production service resource, software toolkit, analysis service resource, software resource, data analysis service | 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 | 2026-08-12 10:51:33 | 13 | |||||||||||
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Mizutani Lab 3D Structure Portal Resource Report Resource Website 1+ mentions |
Mizutani Lab 3D Structure Portal (RRID:SCR_016529) | organization portal, portal, service resource, data or information resource, data repository, storage service resource, 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 | 2026-08-12 10:51:35 | 2 | |||||||||||
|
Marvel Resource Report Resource Website 1+ mentions |
Marvel (RRID:SCR_017621) | image analysis software, software toolkit, software application, data processing software, alignment software, software resource | 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 | 2026-08-12 10:51:52 | 2 | |||||||||||
|
Letswave Resource Report Resource Website 10+ mentions |
Letswave (RRID:SCR_016414) | data visualization software, software toolkit, software application, data processing software, software resource | 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 | 2026-08-12 10:51:30 | 27 | |||||||||
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TSDiffAna Resource Report Resource Website 1+ mentions |
TSDiffAna (RRID:SCR_016656) | image analysis software, software application, data processing software, software resource, data analysis 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 | 2026-08-12 10:51:34 | 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 resource, software application | 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 RR23093; NCRR RR17573 |
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 | 2026-08-12 10:51:37 | 23 | |||||
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Subcellular App Resource Report Resource Website 1+ mentions |
Subcellular App (RRID:SCR_018790) | service resource, software resource, data access protocol, web service | Web interface for simulation of biological molecular networks. Web based environment for creation and simulation of reaction-diffusion models integrated with molecular repository. Allows to import, combine and simulate existing models expressed with BNGL and SBML languages. Application is integrated with number of solvers for reaction-diffusion systems of equations. | Subcellular simulation, reaction-diffusion modeling, brain simulation platform, human brain project, subcellular model, biological molecular network simulation, reaction diffusion model, solver, reaction diffusion system, equation, simulation, molecular network | has parent organization: Human Brain Project EU | Human Brain Project SGA 1-3 | Restricted | SCR_018791 | https://humanbrainproject.github.io/hbp-sp6-guidebook/online_usecases/subcellular_level/subcellular_app/subcellular_app.html | SCR_018790 | Subcellular app, subcellular application, Subcellular Application | 2026-08-12 10:52:13 | 1 | ||||||
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Nutil - Neuroimaging utilities Resource Report Resource Website 10+ mentions |
Nutil - Neuroimaging utilities (RRID:SCR_017183) | Nutil | image analysis software, software toolkit, image processing software, software application, data processing software, software resource | 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 | 2026-08-12 10:51:44 | 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 | organization portal, portal, service resource, data or information resource, database, disease-related portal, topical portal, data repository, storage service resource | 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 | 2026-08-12 10:51:26 | 6 | ||||
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Computer Vision System Toolbox Resource Report Resource Website 1+ mentions |
Computer Vision System Toolbox (RRID:SCR_017581) | software toolkit, image processing software, software application, data processing software, software resource | 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 | 2026-08-12 10:51:47 | 4 | |||||||||
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OrthoFinder Resource Report Resource Website 1000+ mentions |
OrthoFinder (RRID:SCR_017118) | data processing software, data analysis software, software resource, software application | 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 | 2026-08-12 10:51:41 | 3413 | |||||
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UCLA Diffraction Anisotropy Server Resource Report Resource Website 1+ mentions |
UCLA Diffraction Anisotropy Server (RRID:SCR_018722) | service resource, production service resource, analysis service resource, software resource, data access protocol, web service | Web server to indicate severity of anisotropy in data set. Degree of anisotropy is indicated by anisotropic delta B statistic. | Anisotropy, anisotropy severity, anisotropy severity indication, anisotropy degree, anisotropic delta B statistic | has parent organization: University of California at Los Angeles; California; USA | Free, Freely available | SCR_018722 | 2026-08-12 10:52:09 | 8 | ||||||||||
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tximport Resource Report Resource Website 100+ mentions |
tximport (RRID:SCR_016752) | data processing software, data analysis software, software resource, software application | 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 |
SNSF 143883; European Commission ; NCI T32 CA009337 |
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 | 2026-08-12 10:51:31 | 100 | ||||
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SuperSegger Resource Report Resource Website 1+ mentions |
SuperSegger (RRID:SCR_018532) | image analysis software, software toolkit, software application, data processing software, software resource | Software package as automated MATLAB based trainable image cell segmentation, fluorescence quantification and analysis suite. Used for high throughput time lapse fluorescence microscopy of in vivo bacterial cells. Robust image segmentation, analysis and lineage tracking of bacterial cells. | Image cell segmentation, fluorescence quantification, data analysis, high throughput, time lapse, fluorescence microscopy, bacteria cell, image segmentation |
is related to: MATLAB has parent organization: University of Washington; Seattle; USA |
University of Washington Royalty Research Fund ; Sloan BR2011‐110; NSF PHY‐084845; NSF MCB‐1151043‐CAREER; Danish National Research Foundation |
PMID:27569113 | Free, Available for download, Freely available | https://github.com/wiggins-lab/SuperSegger | SCR_018532 | 2026-08-12 10:52:10 | 3 |
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