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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Leica: TCS SPE Resource Report Resource Website 10+ mentions |
Leica: TCS SPE (RRID:SCR_002140) | TCS SPE | instrument resource | High resolution, compact and robust confocal that enables immunohistochemical colocalization analysis of florescent markers. Leica TCS SPE confocal point-scanning, spectral system for fluorescence imaging of live or fixed cells. | confocal microscope, imaging, instrument, equipment, hardware | has parent organization: Leica Microsystems | Restricted | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/main/PDF/SCR_002140.pdf | SciRes_000154 | http://www.leica-microsystems.com/fileadmin/downloads/Leica%20TCS%20SPE/Brochures/Leica%20TCS%20SPE-Brochure_EN.pdf | SCR_002140 | Leica TCS SPE confocal microscope | 2026-07-25 12:05:17 | 32 | |||||
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miso-lims Resource Report Resource Website 10+ mentions |
miso-lims (RRID:SCR_002259) | MISO | software resource | Open source software for a Laboratory Information Management System (LIMS) for NGS sequencing centres. | laboratory information management system, ngs sequencing, lims | is listed by: OMICtools | Open Source, Free | OMICS_01007 | SCR_002259 | MISO: An open-source LIMS for NGS sequencing centres, MISO: An open source LIMS for small-to-large scale sequencing centres | 2026-07-25 12:05:19 | 20 | |||||||
|
flowFit Resource Report Resource Website 1+ mentions |
flowFit (RRID:SCR_002286) | software resource | A Bioconductor package designed to perform quantitative analysis of cell proliferation in tracking dye-based experiments. The package uses an R implementation of the Levenberg-Marquardt algorithm (minpack.lm) to fit a set of peaks (corresponding to different generations of cells) over the proliferation-tracking dye distribution in a FACS experiment. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24681909 | Artistic License, v2 | OMICS_05601 | SCR_002286 | flowFit - Estimate proliferation in cell-tracking dye studies | 2026-07-25 12:05:19 | 4 | |||||||
|
spliceR Resource Report Resource Website 10+ mentions |
spliceR (RRID:SCR_002280) | software resource | An easy-to-use R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. | standalone software, unix/linux, mac os x, windows, c, r, differential expression, high throughput sequencing, rna-seq, rna-seq, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24655717 | GNU General Public License, v2 or greater | OMICS_03514 | SCR_002280 | spliceR - Classification of alternative splicing and prediction of coding potential from RNA-seq data | 2026-07-25 12:05:19 | 25 | |||||||
|
neuRosim Resource Report Resource Website 10+ mentions |
neuRosim (RRID:SCR_002154) | neuRosim | software resource | Software package that allows users to generate fMRI time series or 4D data. Some high-level functions are created for fast data generation with only a few arguments and a diversity of functions to define activation and noise. For more advanced users it is possible to use the low-level functions and manipulate the arguments. | r, fmri, time series, 4d | has parent organization: CRAN | Free, Available for download, Freely available | SciRes_000194 | SCR_002154 | neuRosim: Functions to Generate fMRI Data Including Activated Data Noise Data and Resting State Data | 2026-07-25 12:05:20 | 20 | |||||||
|
BD Biosciences: LSR II Flow Cytometer Resource Report Resource Website 10+ mentions |
BD Biosciences: LSR II Flow Cytometer (RRID:SCR_002159) | LSR II Flow Cytometer | instrument resource | Benchtop high-performance cell sorter with multiple lazer, detector and fluoroscrome options. Allows detection of 12 parameters (10 color conjugates, forward and sideward scatter). | flow cytometer, instrument, equipment, hardware | has parent organization: BD Biosciences | THIS RESOURCE IS NO LONGER IN SERVICE | https://drive.google.com/file/d/1iqsXa8XNCYWutCswBRYBWluHGag0lOSx/view?usp=drivesdk | Model_Number_BD LSR II, SciRes_000152 | https://fccf.sitehost.iu.edu/pdf/BDLSRIIUserGuide.pdf | http://www.rockefeller.edu/fcrc/pdf/BD_LSRII_Brochure_SJ-0142-00.pdf | SCR_002159 | 2026-07-25 12:05:16 | 35 | |||||
|
FR-HIT Resource Report Resource Website 10+ mentions |
FR-HIT (RRID:SCR_002181) | FR-HIT | software resource | An efficient fragment recruitment software program for next generation sequences against microbial reference genomes. It produces similar sensitivity of BLASTN, but runs at a 100 times higher speed. The algorithm adopts a seeding heuristic strategy with overlapping k-mer hashing to locate candidate matching blocks on the reference sequences, and then apply an effective filtering within the candidate blocks to filter out blocks that do not meet the minimum criteria for containing an alignment with specified parameters. For each candidate block that passed the filter, the best matching sub-regions between a candidate block and a read are determined, and used subsequently by the banded Smith-Waterman algorithm to carry out the actual alignment efficiently, which will finally verify if this can be a valid recruitment hit. | metagenomics, bioinformatics, sequence analysis, next-generation sequencing |
is listed by: OMICtools has parent organization: Google Code |
Free, Freely available | OMICS_01850 | SCR_002181 | FR-HIT: Metagenome Fragment Recruitment at High Identity with Tolerance, Metagenome Fragment Recruitment at High Identity with Tolerance, Fragment Recruitment at High Identity with Tolerance | 2026-07-25 12:05:21 | 11 | |||||||
|
metaRNASeq Resource Report Resource Website 10+ mentions |
metaRNASeq (RRID:SCR_002174) | software resource | Software package for meta-analysis of RNA-seq data. This package implements two p-value combination techniques (inverse normal and Fisher methods). It also provides a vignette explaining how to combine data from multiple RNA-seq experiments. | standalone software, unix/linux, mac os x, windows, r |
is listed by: OMICtools is related to: SMAGEXP has parent organization: CRAN |
PMID:24678608 | Free, Available for download, Freely available | OMICS_03527 | SCR_002174 | metaRNASeq: Meta-analysis of RNA-seq data | 2026-07-25 12:05:21 | 30 | |||||||
|
Genoscope Resource Report Resource Website 100+ mentions |
Genoscope (RRID:SCR_002172) | Genoscope | institution | French national sequencing center with the following resources: * Sequencing ** Genoscope Projects * Environmental genomics ** Microbial diversity in wastewater ** Metabolic genomics * Bioinformatics ** Atelier for comparative genomics ** Computational Systems Biology ** Servers resources *** GGB for Generic Genome Browser: graphic interface for various databases (sequence, annotation, syntenies...) for a given organism. *** MaGe for Magnifying Microbial Genomes: annotation system for microbial genomes. | environmental genomics, biocatalysis, environment, genomics, sequencing, bioinformatics, biodiversity, blast, blat, ggb, mage, metabolic, whole genome shotgun, chromosome 3, cdna, chromosome 14, alternative splicing, o��kopleura dioica, mutation, enzymatic cloning, screening, synteny, data set, genome, sequence, annotation, genome browser, FASEB list | has parent organization: CEA; Gif sur Yvette; France | Free, Freely available | ISNI: 0000 0004 0641 2997, Wikidata: Q3100800, grid.434728.e, nif-0000-20957 | https://ror.org/028pnqf58 | SCR_002172 | Genoscope - Centre National de S�quen�age, Genoscope - French National Sequencing Center, French National Sequencing Center, Genoscope - Centre National de Sequencage | 2026-07-25 12:05:17 | 158 | ||||||
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DEMI Resource Report Resource Website 1+ mentions |
DEMI (RRID:SCR_002291) | software resource | R package for estimating differential expression from multiple indicators that capitalizes on the high number of concurrent measurements. It extends to various experimental designs and target categories (transcripts, genes, genomic regions) as well as small sample sizes. | standalone software, affymetrix, mac os x, unix/linux, windows, r |
is listed by: OMICtools has parent organization: CRAN |
PMID:24586062 | Free, Available for download, Freely available, Acknowledgement requested | OMICS_03438 | http://cran.r-project.org/web/packages/demi/ | SCR_002291 | demi: Differential Expression from Multiple Indicators, Differential Expression from Multiple Indicators | 2026-07-25 12:05:23 | 6 | ||||||
|
flowCore Resource Report Resource Website 100+ mentions |
flowCore (RRID:SCR_002205) | software resource | A Bioconductor software package for high throughput flow cytometry that provides S4 data structures and basic functions. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, infrastructure |
is used by: flowBeads is listed by: OMICtools has parent organization: Bioconductor |
PMID:19358741 | Artistic License, v2 | OMICS_05596 | SCR_002205 | flowCore: Basic structures for flow cytometry data | 2026-07-25 12:05:21 | 350 | |||||||
|
CIGAL Resource Report Resource Website 1+ mentions |
CIGAL (RRID:SCR_002232) | CIGAL | software resource | Software program that provides accurate real-time stimulus control, behavioral and physiological recording, and synchronization with external devices. It can also provide continuous real-time feedback of task performance and physiological responses. Task programming typically involves a simple text file specifying basic parameter settings (e.g. screen color) and a list of stimulus events, which can include images, animated movies, sound files, text stimuli, video graphics, or commands that communicate with external hardware devices. Multiple video and auditory stimuli can be presented simultaneously. Multi-channel response recording and real-time feedback features require no user programming. Advanced users can add customized stimulus events using CIGAL's real-time programming capabilities. Output files can be automatically created in a variety of output formats (e.g. FSL 3-column files, XML Events files, CSV trial tables). | magnetic resonance, stimulus control, behavioral recording, physiological recording |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: Duke University; North Carolina; USA |
Free, Available for download, Freely available | nlx_155528 | http://www.nitrc.org/projects/cigal | http://fourier.biac.duke.edu/wiki/doku.php/jvs:cigal | SCR_002232 | Compilable Imaging Graphics and Analytical Language | 2026-07-25 12:05:19 | 6 | |||||
|
NIfTImatlab Resource Report Resource Website 1+ mentions |
NIfTImatlab (RRID:SCR_002230) | NIfTImatlab | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 28, 2025. Software tool that allows the user to operate on NIfTI image files from Matlab. | matlab, nifti, image | has parent organization: New York University; New York; USA | THIS RESOURCE IS NO LONGER IN SERVICE | nlx_155526 | SCR_002230 | NYU CBI NIfTI Matlab tool | 2026-07-25 12:05:18 | 1 | |||||||
|
4D Atlases Construction Resource Report Resource Website 1+ mentions |
4D Atlases Construction (RRID:SCR_002227) | software resource | Software package for constructing longitudinal atlases, which are the necessary steps for many brain-related applications. | magnetic resonance, altas, brain, software package |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) has parent organization: University of North Carolina at Chapel Hill School of Medicine; North Carolina; USA |
PMID:34891818 PMID:31115143 |
Free, Available for download, Freely available | nlx_155688 | http://www.nitrc.org/projects/atlas4d | http://www.med.unc.edu/bric/ideagroup/free-softwares/4d-atlases-construction | SCR_002227 | 4D Atlas Construction Toolbox, 4D Atlas Construction | 2026-07-25 12:05:18 | 1 | |||||
|
Multi-Modal MRI Reproducibility Resource Resource Report Resource Website 10+ mentions |
Multi-Modal MRI Reproducibility Resource (RRID:SCR_002442) | Multi-Modal MRI Reproducibility Resource | image collection, data or information resource | Scan-rescan imaging sessions on 21 healthy volunteers (no history of neurological disease) intended to be a resource for statisticians and imaging scientists to be able to quantify the reproducibility of their imaging methods using data available from a generic 1 hour session at 3T. Imaging modalities include MPRAGE, FLAIR, DTI, resting state fMRI, B0 and B1 field maps, ASL, VASO, quantitative T1 mapping, quantitative T2 mapping, and magnetization transfer imaging. All data have been converted to NIFTI format. Please cite: Bennett. A. Landman, Alan J. Huang, Aliya Gifford, Deepti S. Vikram, Issel Anne L. Lim, Jonathan A.D. Farrell, John A. Bogovic, Jun Hua, Min Chen, Samson Jarso, Seth A. Smith, Suresh Joel, Susumu Mori, James J. Pekar, Peter B. Barker, Jerry L. Prince, and Peter C.M. van Zijl. ?Multi-Parametric Neuroimaging Reproducibility: A 3T Resource Study?, NeuroImage. (2010) NIHMS/PMC:252138 doi:10.1016/j.neuroimage.2010.11.047 | java image science toolkit, magnetic resonance, nifti, neuroimaging, reproducibility, mprage, flair, dti, resting state fmri, b0 field map, b1 field map, asl, vaso, quantitative t1 mapping, quantitative t2 mapping, magnetization transfer imaging |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: JIST: Java Image Science Toolkit |
Healthy | PMID:21094686 | Free, Available for download, Freely available | nlx_155818 | SCR_002442 | 2026-07-25 12:05:26 | 11 | ||||||
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Cogprints: Cognitive Sciences EPrint Archive Resource Report Resource Website 1+ mentions |
Cogprints: Cognitive Sciences EPrint Archive (RRID:SCR_002314) | journal article | An electronic archive for self-archive papers in any area of Psychology, neuroscience, and Linguistics, and many areas of Computer Science, Philosophy, Biology, Medicine, Anthropology, cognitive ethnology, archeology, paleontology, as well as any other portions of the physical, social and mathematical sciences that are pertinent to the study of cognition. | ethnology, anthropology, archeology, biology, cognition, cognitive science, computer science, linguistics, mathematical, medicine, neuroscience, paleontology, philosophy, physical, psychology, science, scientific literature databases and services, social | has parent organization: University of Southampton; Southampton; United Kingdom | nif-0000-21093 | SCR_002314 | Cogprints | 2026-07-25 12:05:20 | 3 | |||||||||
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flowCyBar Resource Report Resource Website 1+ mentions |
flowCyBar (RRID:SCR_002319) | software resource | A software package to analyze flow cytometric data using gate information to follow population / community dynamics. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry, clustering, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
GNU General Public License, v2 | OMICS_05597 | SCR_002319 | flowCyBar - Analyze flow cytometric data using gate information | 2026-07-25 12:05:20 | 5 | ||||||||
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VS-Lite Resource Report Resource Website 1+ mentions |
VS-Lite (RRID:SCR_002431) | VS-Lite | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2023. A simple, efficient, process-based forward model of tree-ring growth, requires as inputs only latitude and monthly temperature and precipitation. | model, mathematical model, tree ring, dendrochronology, tree ring width, tree, ring, ring growth model |
is listed by: CINERGI has parent organization: World Data Center for Paleoclimatology |
NOAA ; NSF 0724802 |
THIS RESOURCE IS NO LONGER IN SERVICE. | SciRes_000128 | SCR_002431 | Vaganov-Shashkin-Lite, Vaganov-Shashkin-Lite Model of Tree-Ring Width | 2026-07-25 12:05:22 | 2 | ||||||
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ANOVA Resource Report Resource Website 100+ mentions |
ANOVA (RRID:SCR_002427) | ANOVA | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2023. Matlab code for two-factor (location and year) analysis-of-variance model for the calculation of climate anomalies, in which the reference interval is specified as the full length of the dataset. This scheme avoids the affects of shorter (e.g. 1961-1990) reference intervals on the temporal evolution of the spatial standard deviation of climate anomalies. Data files provided. | model program, anomaly, anomaly, climate, variance, climate anomaly, matlab |
is listed by: CINERGI has parent organization: World Data Center for Paleoclimatology |
PMID:27406694 PMID:15866832 |
THIS RESOURCE IS NO LONGER IN SERVICE. | SciRes_000129 | SCR_002427 | Analysis of Variance | 2026-07-25 12:05:22 | 343 | ||||||
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DWGSIM Resource Report Resource Website 50+ mentions |
DWGSIM (RRID:SCR_002342) | DWGSIM | software resource | Whole Genome Simulator for Next-Generation Sequencing. | next-generation sequencing, whole genome simulation |
is listed by: OMICtools is listed by: Debian |
GNU General Public License, v2 | OMICS_00249 | https://sources.debian.org/src/dwgsim/ | SCR_002342 | 2026-07-25 12:05:20 | 51 |
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