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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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HiCRes Resource Report Resource Website 1+ mentions |
HiCRes (RRID:SCR_022319) | software application, simulation software, software resource | Software pipeline to estimate and predict genomic resolution of Hi-C libraries. Used for estimating and predicting HiC library resolution. | Hi-C libraries, 3D chromatin interactions genome wide measurement, estimate resolution of dataset, genomic resolution | NEI ZIAEY000450; NEI ZIAEY000546 |
DOI:10.1093/nar/gkab1235 | Free, Available for download, Freely available | https://github.com/ClaireMarchal/HiCRes | SCR_022319 | 2026-08-11 09:44:20 | 1 | ||||||||
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JUMP Cell Painting Consortium Resource Report Resource Website 1+ mentions |
JUMP Cell Painting Consortium (RRID:SCR_021868) | data or information resource, consortium, portal, organization portal | Consortium is creating new data driven approach to drug discovery based on cellular imaging, image analysis, and high dimensional data analytics. Creates public data set to validate and scale up this image based drug discovery strategy. By coordinating assay procedures across partners, future created data will be well matched. Aims to make cell images as computable as genomes and transcriptomes. | creating new data, drug discovery, cellular imaging, image analysis, high dimensional data analytics, | has parent organization: Broad Institute | Free, Freely available | SCR_021868 | JUMP-Cell Painting Consortium | 2026-08-11 09:44:16 | 2 | |||||||||
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CytoMAP Resource Report Resource Website 10+ mentions |
CytoMAP (RRID:SCR_021227) | data analysis software, software application, software toolkit, software resource, data processing software, data analytics software | Software tool as spatial analysis software for whole tissue sections.Utilizes information on cell type and position to phenotype local neighborhoods and reveal how their spatial distribution leads to generation of global tissue architecture.Used to make advanced data analytic techniques accessible for single cell data with position information. | Histo cytometric multidimensional, analysis pipeline, whole tissue sections, spatial analysis, single cell data with position information, phenotype local neighborhoods, global tissue architecture | has parent organization: Washington University School of Medicine in St. Louis; Missouri; USA | NIAID R01 AI134713; NIAID R21 AI142667; NIAID R01 AI134246; NIAID R01 AI076327; NIAID U19 AI135976; NIAID T32 AI10667; NIGMS T32 GM007270; NICHD T32 HD007233; NSF DGE 1762114 |
PMID:32320656 | Free, Available for download, Freely available | SCR_021227 | Histo-Cytometric Multidimensional Analysis Pipeline | 2026-08-11 09:44:10 | 23 | |||||||
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OptiType Resource Report Resource Website 50+ mentions |
OptiType (RRID:SCR_022279) | data analysis software, data processing software, software resource, software application | Software tool for precision HLA typing from next generation sequencing data. | Precision HLA typing, next generation sequencing data, HLA typing, NGS data |
is listed by: Debian is listed by: OMICtools |
German Research Foundation ; German Federal Ministry of Education and Research |
PMID:25143287 | Free, Available for download, Freely available | OMICS_05461 | https://sources.debian.org/src/optitype/ | SCR_022279 | 2026-08-11 09:44:19 | 50 | ||||||
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NF Data Portal Resource Report Resource Website 1+ mentions |
NF Data Portal (RRID:SCR_021683) | portal, service resource, data or information resource, storage service resource, data repository | Portal created to help openly explore and share NF datasets, analysis tools, resources, and publications related to neurofibromatosis and schwannomatosis.Public data repository that stores and shares data generated by multiple collaborative research programs focused on neurofibromatosis diseases. | Sage Bionetworks, NF datasets, neurofibromatosis data, schwannomatosis data, neurofibromatosis diseases | uses: Synapse | neurofibromatosis type 1 (NF1), neurofibromatosis type 2 (NF2), and schwannomatosis (SCH) | Childrens Tumor Foundation ; Neurofibromatosis Therapeutic Acceleration Program |
PMID:31836719 | Free, Freely available | r3d100013571 | https://doi.org/10.17616/R31NJMYR | SCR_021683 | Neurofibromatosis Data Portal | 2026-08-11 09:44:14 | 5 | ||||
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LMAS Resource Report Resource Website 1+ mentions |
LMAS (RRID:SCR_022251) | software application, image reconstruction software, image analysis software, software resource, data processing software | Automated workflow enabling benchmarking of traditional and metagenomic prokaryotic de novo assembly software using defined mock communities. Results are presented in interactive HTML report where selected global and reference specific performance metrics can be explored. | Shotgun metagenomics, genomic assembler | has parent organization: Ben-Gurion University of the Negev; Beer-Sheva; Israel | Free, Available for download, Freely available | SCR_022251 | Last (Meta)Genomic Assembler Standing | 2026-08-11 09:44:19 | 1 | |||||||||
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Subcellular App Resource Report Resource Website 1+ mentions |
Subcellular App (RRID:SCR_018790) | service resource, web service, software resource, data access protocol | 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 | 2026-08-11 09:43:49 | 1 | ||||||
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SNP-sites Resource Report Resource Website 1+ mentions |
SNP-sites (RRID:SCR_022265) | data analysis software, data processing software, software resource, software application | Software tool to find SNP sites from multi-FASTA alignment file. Can output results in multiple formats for downstream analysis. | find SNP sites, Single Nucleotide Polymorphisms, single nucleotide polymorphisms extracting, large whole genome alignment, | Free, Available for download, Freely available | https://github.com/sanger-pathogens/snp-sites | SCR_022265 | Single Nucleotide Polymorphisms-sites | 2026-08-11 09:44:19 | 3 | |||||||||
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purge dups Resource Report Resource Website 500+ mentions |
purge dups (RRID:SCR_021173) | data analysis software, data processing software, software resource, software application | Software tool to purge haplotigs and overlaps in assembly based on read depth.Used for haplotypic duplication identification. Designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth. | haplotypic duplication identification, remove haplotigs overlap, remove contig overlaps, de novo assembly, read depth | Free, Available for download, Freely available | SCR_021173 | purge_dups | 2026-08-11 09:44:08 | 503 | ||||||||||
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UCLA Diffraction Anisotropy Server Resource Report Resource Website 1+ mentions |
UCLA Diffraction Anisotropy Server (RRID:SCR_018722) | service resource, analysis service resource, web service, software resource, production service resource, data access protocol | 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 | 2026-08-11 09:44:00 | 8 | ||||||||||
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UMI4Cats Resource Report Resource Website 1+ mentions |
UMI4Cats (RRID:SCR_021780) | data analysis software, software application, software resource, data processing software, data visualization software | Software R package for analyzing UMI-4C chromatin contact data. Used to analyze chromatin contact profiles obtained by UMI-4C. | Profile and quantitatively compare, targeted chromosomal contact profiles, unique molecular identifiers, combines chromosome conformation capture | DOI:10.1093/bioinformatics/btab392 | Free, Available for download, Freely available | https://bioconductor.org/packages/UMI4Cats/, https://github.com/Pasquali-lab/UMI4Cats | SCR_021780 | Unique Molecular Identifiers combines chromosome conformation capture | 2026-08-11 09:44:15 | 2 | ||||||||
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Computational Analysis of gene Family Evolution Resource Report Resource Website 10+ mentions |
Computational Analysis of gene Family Evolution (RRID:SCR_018924) | CAFE | data analysis software, data processing software, software resource, software application | Software tool for computational analysis of gene family evolution. Used for statistical analysis of evolution gene family sizes. Models evolution of gene family sizes over phylogeny. | Computational analysis, gene family evolution, evolution statistical analysis, gene family size, gene evolution, phylogeny | has parent organization: Indiana University; Indiana; USA | NHGRI R33 HG003070; NSF MCB 0528465; METACyt Initiative of Indiana University ; Lilly Endowment ; Inc |
PMID:16543274 | SCR_018924 | CAFE v2.0, CAFE v4.0, CAFE v3.0, CAFE v5.0, Computational Analysis of gene Family Evolution | 2026-08-11 09:43:50 | 17 | |||||||
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SuperSegger Resource Report Resource Website 1+ mentions |
SuperSegger (RRID:SCR_018532) | software application, software toolkit, image analysis software, software resource, data processing software | 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 | 2026-08-11 09:43:59 | 3 | |||||||
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Mouse Action Recognition System Resource Report Resource Website 1+ mentions |
Mouse Action Recognition System (RRID:SCR_022347) | MARS | data analysis software, data processing software, software resource, software application | Software Python pipeline for automated detection, pose estimation, and behavior classification in socially interacting mice.Used for pose estimation and behavior quantification in pairs of freely behaving mice. | OpenBehavior, behavior measurement, video analysis, real time recording and analysis, pose estimation and behavior quantification, freely behaving mice |
is listed by: OpenBehavior is related to: MARS Developer has parent organization: Northwestern University; Illinois; USA |
DOI:10.7554/eLife.63720 | Free, Available for download, Freely available | https://github.com/neuroethology/MARS | SCR_022347 | 2026-08-11 09:44:21 | 8 | |||||||
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triku Resource Report Resource Website 1+ mentions |
triku (RRID:SCR_020977) | data analysis software, data processing software, software resource, software application | Software tool as feature selection method based on nearest neighbors for single-cell data. | Selection method, nearest neighbors, single cell data, data analysis | uses: scanpy | Free, Available for download, Freely available | https://triku.readthedocs.io/en/latest/ | SCR_020977 | 2026-08-11 09:44:08 | 2 | |||||||||
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DrivAER Resource Report Resource Website 1+ mentions |
DrivAER (RRID:SCR_019076) | data analysis software, data processing software, software resource, software application | Software tool as method for identification of driving transcriptional programs based on AutoEncoder derived Relevance scores. Infers relevance scores for transcriptional programs with respect to specified outcomes of interest in single-cell RNA sequencing data, such as psuedotemporal ordering or disease status.Used for manifold interpretation in scRNA-seq data. | Manifold interpretation, scRNAseq data, relevance scores infering, transcriptional program, psuedotemporal ordering, disease status, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:drivaer | https://bio.tools/drivaer | SCR_019076 | Driving transcriptional programs using AutoEncoder based Relevance scores | 2026-08-11 09:44:06 | 1 | |||||||
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AutoStereota Resource Report Resource Website 1+ mentions |
AutoStereota (RRID:SCR_022330) | portal, project portal, data or information resource, instrument resource | Automated surgical instrument for brain tissue aspiration.Instrument for microendoscope implantation. Utilizes robotic control of needle connected to vacuum pump to aspirate brain tissue. System consists of robotic surgical instrument built around commercially available stereotaxic instrument and open source MATLAB-based GUI for control. | OpenBehavior, Instrument, brain tissue aspiration, microendoscope implantation | is listed by: OpenBehavior | DOI:10.1016/j.jneumeth.2018.10.013 | Free, Freely available | https://github.com/liang-bo/AutoStereota | SCR_022330 | 2026-08-11 09:44:21 | 3 | ||||||||
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STENCIL Resource Report Resource Website 1+ mentions |
STENCIL (RRID:SCR_021878) | software application, data processing software, software resource, data visualization software | Web engine for visualizing and sharing life science datasets.Designed to organize, visualize, and enable sharing of interactive genomic data visualizations. Provides ability to inspect and interpret sequencing data, without requiring programming expertise. | Visualizing genomic data, sharing genomic data, interactive genomic data visualizations, interpret sequencing data | NIEHS ES013768; NIGMS GM125722 |
DOI:10.1101/2021.06.04.447108 | Free, Available for download, Freely available | SCR_021878 | 2026-08-11 09:44:14 | 4 | |||||||||
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Genomic Association Tester Resource Report Resource Website 10+ mentions |
Genomic Association Tester (RRID:SCR_020949) | GAT | data analysis software, software application, software resource, simulation software, data processing software | Software tool as simulation framework for testing association of genomic intervals. Used for estimating significance of overlap between multiple sets of genomic intervals. Estimates statistical significance based on simulation and controls for multiple tests using false discovery rate. | Genomic intervals, genomic intervals association testing, overlap significance estimation, genomic intervals sets, segment length distribution, chromosomal location, isochores | UK Medical Research Council | PMID:23782611 | Free, Available for download, Freely available | https://github.com/AndreasHeger/gat | http://code.google.com/p/genomic-association-tester | SCR_020949 | 2026-08-11 09:43:58 | 31 | ||||||
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PM4NGS Resource Report Resource Website 1+ mentions |
PM4NGS (RRID:SCR_019164) | data analysis software, software application, data management software, software toolkit, workflow software, software resource, data processing software | Software tool to generate standard organizational structure for Next Generation Sequencing data analysis. Includes directory structure for project, several Jupyter notebooks for data management and CWL workflows for pipeline execution. | NGS workflow, standard organizational structure generation, Next Generation Sequencing data, NGS data analysis, NGS data analysis workflow, data integration, Jupyter notebook, CWL format, bio.tools |
is listed by: bio.tools is listed by: Debian |
Intramural Research Program of the National Library of Medicine NIH | DOI:10.7490/f1000research.1117155.1 | Free, Freely available | biotools:pm4ngs | https://bio.tools/pm4ngs | SCR_019164 | Project Manager for Next Generation Sequencing | 2026-08-11 09:44:07 | 1 |
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