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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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OmicsBean Resource Report Resource Website 100+ mentions |
OmicsBean (RRID:SCR_016322) | software application, software resource, data analytics software, data analysis software, data processing software | Software tool for multi-omics data analysis that can perform complex and personalized analysis. Network regulation and molecular mechanism models can be customized according to the requirements of the users. | GeneForHealth Biotech Inc (GFK), data, analysis, genome, proteome, metabolome, network, molecular, mechanism, model, collect, store, analytic, multi, omic | Commercially available, Demo available | SCR_016322 | 2026-02-11 10:59:27 | 145 | |||||||||||
|
ANNOgesic Resource Report Resource Website 10+ mentions |
ANNOgesic (RRID:SCR_016326) | software application, software resource, software toolkit, data analysis software, standalone software, data processing software | Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data. | bacterial, archaeal, RNA, sequencing, data, analysis, genome, annotation, statistic, visualization, protein, interaction, prediction, grouping, go, ontology, gene, differential, circular |
is related to: Infernal is related to: Vienna RNA is related to: Biopython is related to: MEME Suite - Motif-based sequence analysis tools is related to: Segemehl |
Free, Freely available, Available for download | SCR_016326 | 2026-02-11 10:59:27 | 10 | ||||||||||
|
MetaCyto Resource Report Resource Website 1+ mentions |
MetaCyto (RRID:SCR_016415) | software application, software resource, software toolkit, data analysis software, data processing software | Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database. | automated, analysis, meta, flow, cytometry, data, bio.tools |
is listed by: Bioconductor is listed by: NIDDK Information Network (dkNET) is listed by: bio.tools is listed by: Debian is related to: The Immunology Database and Analysis Portal (ImmPort) |
the National Institute of Allergy and Infectious Diseases HHSN272201200028C | Free, Available for download, Freely available | biotools:metacyto | https://bio.tools/metacyto | SCR_016415 | 2026-02-11 10:59:27 | 5 | |||||||
|
CycIF.org Resource Report Resource Website 10+ mentions |
CycIF.org (RRID:SCR_016267) | CycIF.org | data or information resource, immunofluorescence, narrative resource, experimental protocol, web page, immuno detection protocol | Web page for cyclic immunofluorescence. It lists several downloadable data and software pertaining to cyclic immunofluorescence. | immunofluorescence, cyclic, cycif, data, software, single cell, numeric, dataset, intratumoural, heterogeneity | has parent organization: LINCS Data Portal | NHLBI U54 HL127365 | PMID:26399630 | Public | SCR_016267 | cycif.org | 2026-02-11 10:59:22 | 13 | ||||||
|
OMA Orthology database Resource Report Resource Website 1+ mentions |
OMA Orthology database (RRID:SCR_016425) | OMA | software application, data or information resource, database, software resource, web service, standalone software, data access protocol | Web based database interface for orthology prediction for the inference of orthologs among complete genomes. Used to relate genes across many species., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | interface, orthology, prediction, inference, complete, genome, species, data | Swiss Institute of Bioinformatics ; UK Biotechnology and Biological Sciences Research Council ; University College London ; Bayer Crop Science NV |
PMID:29106550 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_016425 | Orthologous MAtrix | 2026-02-11 10:59:28 | 9 | |||||||
|
kCSD-Matlab Resource Report Resource Website 1+ mentions |
kCSD-Matlab (RRID:SCR_016424) | kCSD | software resource, software application, data processing software, data analysis software | Software tool for analyzing recordings from multielectrodes. Source code for the Matlab implementation of the Kernel Current Source Density method. The method operates in one-, two-, and three-dimensional space to perform nonparametric estimation of transmembrane current sources from local field potentials recorded from arbitrarily distributed electrodes. | analyzing, recording, data, multielectrode, transmembrane, current, source, estimate, kernel, source, density, method | is related to: MATLAB | Free, Available for download, Freely available | SCR_016424 | kernel Current Source Density | 2026-02-11 10:59:31 | 2 | ||||||||
|
BIOQUANT Life Science Resource Report Resource Website 10+ mentions |
BIOQUANT Life Science (RRID:SCR_016423) | software application, image analysis software, software resource, software toolkit, data analysis software, data processing software | Software tool to collect and analyse data on images of tissue slides or welled plates.Supports high-throughput immunofluorescence and immunohistochemistry, stereology, densitometry, and 3D modeling. Used in bioscience research in animal models and human biopsy, developmental neuroscience, traumatic brain/spinal cord injury, glaucoma, eye-movement disorders, cardiovascular disease and muscle disorders. | BioQuant Inc., collect, analyse, data, tissue, slide, well, plate, capture, camera, scanned, image, immunofluorescence, immunohistochemistry, stereology, densitometry, 3D modeling | Commercially available, Tutoring available | SCR_016423 | 2026-02-11 10:59:29 | 19 | |||||||||||
|
YAMP Resource Report Resource Website 1+ mentions |
YAMP (RRID:SCR_016236) | software application, software resource, data analysis software, sequence analysis software, data processing software | Software for processing and analysis of sequencing data. It has a strong focus on quality control, timely processing, functional annotation, and portability. | metagenomics, reproducibility, workflow, containerization, sequencing, gene, rna, annotating, portable, data, process | Free, Available for download | SCR_016236 | YAMP: Yet Another Metagenomic Pipeline, Yet Another Metagenomic Pipeline (YAMP), Yet Another Metagenomic Pipeline | 2026-02-11 10:59:21 | 7 | ||||||||||
|
Deeptools Resource Report Resource Website 1000+ mentions |
Deeptools (RRID:SCR_016366) | software application, data visualization software, software resource, software toolkit, data analysis software, data processing software | Python based tools to process, visualize and analyse high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Implemented within Galaxy framework. Used to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. | process, visualize, analysis, sequencing, data, ChIP-seq, RNA-seq, MNase-seq, quality, control, normalization, aligned, read, clustering, bioinformatic | works with: Galaxy | German Research Foundation SFB 992; German Epigenome Programme DEEP 01KU1216G |
PMID:27079975 | Free, Available for download, Freely available | http://deeptools.ie-freiburg.mpg.de/ | SCR_016366 | 2026-02-11 10:59:28 | 2418 | |||||||
|
SMAGEXP Resource Report Resource Website 1+ mentions |
SMAGEXP (RRID:SCR_016360) | SMAGEXP | software application, software resource, software toolkit, data analysis software, data processing software | Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more. | transcriptomics, data, meta, analysis, MicroArrays, RNA-Seq, Galaxy, gene, expression, next, generation, sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Galaxy is related to: Gene Expression Omnibus is related to: metaMA is related to: metaRNASeq |
PMID:30698691 | Free, Available for download, Freely available | biotools:SMAGEXP | https://bio.tools/SMAGEXP | SCR_016360 | Statistical Meta Analysis for Gene EXPression | 2026-02-11 10:59:30 | 2 | |||||
|
XLSTAT Resource Report Resource Website 100+ mentions |
XLSTAT (RRID:SCR_016299) | XLSTAT | software application, data visualization software, data management software, software resource, data analysis software, data processing software | Software for commercial data analysis and statistical software package for Microsoft Excel. | data, process, manage, analyze, visualize, graph, statistic, microsoft, excel | is related to: Microsoft Excel | Addinsoft | Commercially available, Trial available | SCR_016299 | XL STATistics | 2026-02-11 10:59:27 | 146 | |||||||
|
TraCeR Resource Report Resource Website 10+ mentions |
TraCeR (RRID:SCR_016338) | software application, simulation software, software resource, software toolkit, data analysis software, data processing software | Software application for recovery of T cell receptor (TCR) data from single cell data. Used to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. Links T cell specificity with functional response by revealing clonal relationships between cells alongside their transcriptional profiles. | recovery, receptor, single, cell, data, computation, method, reconstruct, sequence, T lymphocyte, RNA, sequence |
is related to: Wellcome Trust Sanger Institute; Hinxton; United Kingdom is related to: European Bioinformatics Institute |
European Research Council ; the Lister Institute for Preventative Medicine (S.A.T.) |
PMID:26950746 | Free, Available for download, Freely available | SCR_016338 | 2026-02-11 10:59:30 | 13 | ||||||||
|
migec Resource Report Resource Website 1+ mentions |
migec (RRID:SCR_016337) | MIGEC | software application, software resource, software toolkit, data analysis software, data processing software | Software package for analysis of immune repertoire sequencing data. Used for recovery of T Cell Receptor ( TCR ) data from bulk population data.Used for high-throughput sequencing data analysis. Allows for error correction while preserving the natural diversity of complex immune repertoires. | high sequencing, molecular, identifier, guided, error, correction, data, analysis, immune, recovery, T cell receptor, | Molecular and Cell Biology program RAS ; Russian Foundation for Basic Research ; Russian President ; European Regional Development Fund |
PMID:24793455 | Free, Available for download, Freely available | SCR_016337 | Molecular Identifier Guided Error Correction | 2026-02-11 10:59:28 | 9 | |||||||
|
clustree Resource Report Resource Website 50+ mentions |
clustree (RRID:SCR_016293) | software application, data visualization software, software resource, data analysis software, data processing software | Software package which allows to produce clustering trees and visualize clusterings at different resolutions. Used in the analysis of large data sets to group together samples with similar properties. | clustering, tree, visualisation, data, set, group, sample, similar, property, different, resolution, cluster | is related to: R Project for Statistical Computing | Free, Freely available, Available for download | https://github.com/lazappi/clustree | SCR_016293 | 2026-02-11 10:59:27 | 82 | |||||||||
|
FLIR tools Resource Report Resource Website 10+ mentions |
FLIR tools (RRID:SCR_016330) | software application, image analysis software, software resource, data analysis software, data processing software | Software application for thermography for FLIR Systems. It has a basic thermal image analysis function including color palette and image adjustment function. Used to analyse the thermographic measurement data. | thermography, FLIR Systems, image, data, measurement, analysis | Free, Available for download | SCR_016330 | 2026-02-11 10:59:28 | 14 | |||||||||||
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star-for-criu Resource Report Resource Website 1+ mentions |
star-for-criu (RRID:SCR_016294) | software application, alignment software, image analysis software, software resource, data processing software | Software as an Hot Start software container for STAR alignment using CRIU (Checkpoint Restore in Userspace) tool to freeze the running container. Can be deployed to align RNA sequencing data. Used in the processing of biomedical big data for better reproducibility and reliability. | hot, start, container, star, aligner, sequencing, data, processing, biomedical, cloud, reproducibility, RNA, analysis, computing, environment | is related to: Systems Transcriptional Activity Reconstruction | NHLBI U54 HL127624; AMEDD Advanced Medical Technology Initiative ; NIGMS R01 GM126019 |
Free, Freely available, Available for download | https://github.com/paizhang/Hotstarting-For-STAR-Alignment | SCR_016294 | 2026-02-11 10:59:29 | 1 | ||||||||
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masked ICA (mICA) Toolbox Resource Report Resource Website 1+ mentions |
masked ICA (mICA) Toolbox (RRID:SCR_016349) | mICA | software application, software resource, software toolkit, data analysis software, data processing software | Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging. | masked, independent, component, analysis, neuroimaging, restricted, subregion, brain, magnetic, resonance, imaging, data, |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: FSL has parent organization: Hannover Medical School; Lower Saxony; Germany |
Horst Görtz Foundation | PMID:27168407 | Free, Freely available, Available for download | SCR_016349 | masked Independent Component Analysis | 2026-02-11 10:59:27 | 1 | ||||||
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LungMap Resource Report Resource Website 50+ mentions |
LungMap (RRID:SCR_016347) | LungMAP | portal, data repository, data or information resource, service resource, storage service resource | Portal for lung histochemistry data. For structural and molecular data regarding normal perinatal and postnatal lung development in the mouse and human. For public sharing of data sets, establishing a repository of young human lung tissues obtained through organ donor organizations, and developing a comprehensive lung ontology .Contains lung images and transcriptomic, proteomic, and lipidomic human and mouse data and provides scientific information to stimulate interest in research careers. Used to serve as a research resource and public education tool. | lung, data, histochemistry, structural, molecular, normal, perinatal, postnatal, development, mouse, human, repository, images, transcriptomic, proteomic, lipidomic |
is related to: RTI International is related to: University of Texas at Austin; Texas; USA is related to: University of Alabama at Birmingham; Alabama; USA is related to: Yale University; Connecticut; USA is related to: University of California at San Diego; California; USA is related to: Carnegie Mellon University; Pennsylvania; USA is related to: Lung Genome Browser |
the National Heart ; Lung ; and Blood Institute of the National Institutes of Health U01HL122638 |
PMID:28798251 | Free, Freely available | SCR_016347 | The Molecular Atlas of Lung Development Program | 2026-02-11 10:59:30 | 52 | ||||||
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iMITS Resource Report Resource Website |
iMITS (RRID:SCR_016552) | iMITS | catalog, data or information resource, database | This resource has been replaced by GenTaR. Software tool for the planning of all IMPC mouse production. Allows IMPC production centers to record the progress of mouse production, cre-excision and to summarise the progress of phenotype data collection and transfer to the IMPC DCC. Stores all the mutation molecular structures made for the IKMC, catalogs of all IKMC products. | international, tracking, system, mouse, production, data, store, catalog, phenotype, collection, mutation, molecular, structure, IKMC, IMPC |
is affiliated with: International Mouse Phenotyping Consortium (IMPC) is related to: GenTaR |
NIH KOMP2; European Union 223592 |
Restricted | SCR_016552 | international Micro Injection Tracking System | 2026-02-11 10:59:32 | 0 | |||||||
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SINCERA Pipeline Resource Report Resource Website 1+ mentions |
SINCERA Pipeline (RRID:SCR_016563) | SINCERA | software application, software resource, data analytics software, data analysis software, data processing software | Software tool implemented in R S4 as an analytic pipeline for processing single-cell RNA-seq data from a whole organ or sorted cells. Used for Single Cell RNA-Seq profiling analysis. | single, cell, RNA seq, data, sorted, whole, organ, profiling, analysis | NHLBI U01 HL110964; NHLBI U01 HL122642; NHLBI R01 HL105433 |
PMID:26600239 | Free, Available for download, Freely available | https://research.cchmc.org/pbge/sincera.html | SCR_016563 | SINCERA, SINgle CEll RNA seq profiling Analysis | 2026-02-11 10:59:26 | 5 |
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