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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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INCell Developer Toolbox Resource Report Resource Website 10+ mentions |
INCell Developer Toolbox (RRID:SCR_015790) | image analysis software, data processing software, software resource, software application | Image analysis software for developing new cellular assay analysis routines. This software provides a selection of advanced segmentation, pre-processing and post-postprocessing tools. | INCell, HCA, cellular assay, advanced segmentation, image analysis, cellular imaging | Commercially available, Available for purchase | SCR_015790 | IN Cell Developer Toolbox v1.6, IN Cell Developer Toolbox | 2026-08-13 09:29:18 | 30 | ||||||||||
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ASIPro Resource Report Resource Website 100+ mentions |
ASIPro (RRID:SCR_014547) | image analysis software, data processing software, software resource, software application | An image analysis software. | image analysis, image analysis software, image processing | SCR_014547 | ASIPro VM | 2026-08-13 09:29:12 | 127 | |||||||||||
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TissueQuest Analysis Software Resource Report Resource Website 10+ mentions |
TissueQuest Analysis Software (RRID:SCR_014822) | image analysis software, data processing software, software resource, software application | Image analysis software for cells and stained areas in samples stained with immunofluorescent markers. | image analysis software, stain, cell, immunofluorescence | is related to: HistoQuest Analysis Software | Commercially available | SCR_014822 | 2026-08-13 09:29:05 | 36 | ||||||||||
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SMIA-CUKIE Resource Report Resource Website 1+ mentions |
SMIA-CUKIE (RRID:SCR_014795) | SMIA | image analysis software, data processing software, software resource, software application | Software used to analyze and quantify images stained with multiple fluorophores in vitro or in vivo. It can output both image and value outputs. | immunofluorescence, image analysis software, fluorophore, image output, value output, bulk process, bulk analyze | DOI:10.5772/21699 | Requires Python 2.7 | SCR_014795 | Simultaneous Multichannel Immunofluorescence Digital Imaging Analyzer, Simultaneous Multichannel Immunofluorescence Analysis | 2026-08-13 09:29:06 | 7 | ||||||||
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National Glycohemoglobin Standardization Program Resource Report Resource Website 500+ mentions |
National Glycohemoglobin Standardization Program (RRID:SCR_015885) | NGSP | data or information resource, portal, project portal | Project that aims to standardize Hemoglobin A1c test results to those of the Diabetes Control and Complications Trial (DCCT) and United Kingdom Prospective Diabetes Study (UKPDS) which established the direct relationships between HbA1c levels and outcome risks in patients with diabetes. | glycohemoglobin, diabetes, dcct, ukpds, hba1c, diabetes patient, hemoglobin, a1c |
is listed by: NIDDK Information Network (dkNET) is listed by: Diabetes Research Centers |
Diabetes | NIDDK UC4 DK096587 | Public | SCR_015885 | NGSP: National Glycohemoglobin Standardization Program | 2026-08-13 09:29:19 | 932 | ||||||
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BASTA Resource Report Resource Website 1+ mentions |
BASTA (RRID:SCR_017303) | software toolkit, data processing software, software resource, software application | Software package as Bayesian method to infer migration from genetic data. Implemented in BEAST2 that combines accuracy of methods based on structured coalescent with computational efficiency required to handle more than few populations. | Bayesian method, infer, migration, genetic, data, structured, coalescent, approximation, population | is related to: BEAST2 | DOI:10.1371/journal.pgen.1005421 | Free, Available for download, Freely available | SCR_017303 | BAyesian STructured coalescent Approximation, BASTA, BEAST2 | 2026-08-13 09:29:41 | 1 | ||||||||
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Science of Behavior Change Research Network Resource Report Resource Website 1+ mentions |
Science of Behavior Change Research Network (RRID:SCR_017385) | SOBC | data or information resource, portal, project portal | Repository for behavioral science measures that have been validated or are in process of being validated in accordance with SOBC Experimental Medicine Approach. | Data, behavioral, science, SOBC, measure, data, medicine | NIH | SCR_017388 | https://scienceofbehaviorchange.org/measures/, https://scienceofbehaviorchange.org/measures/ | SCR_017385 | SOBC Measures Repository, Science of Behavior Change (SOBC) Research Network | 2026-08-13 09:30:02 | 1 | |||||||
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CombineZP Resource Report Resource Website 100+ mentions |
CombineZP (RRID:SCR_014567) | image analysis software, data processing software, software resource, software application | A software used to process stacks of digital images. All of the resulting images are processed to have the same dimensions and then are consolidated into a single image. | digital image, dimension, process stack, digital, dimension modification, image processing, image consolidation | Open Source | SCR_014567 | 2026-08-13 09:29:03 | 137 | |||||||||||
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NIST Mass Spectrometry Data Center Resource Report Resource Website 100+ mentions |
NIST Mass Spectrometry Data Center (RRID:SCR_014680) | data or information resource, organization portal, portal | A data center that develops evaluated mass spectral libraries and provides related software tools that assist compound identification by providing reference mass spectra for GC/MS (by electron ionization) and LC-MS/MS (by tandem mass spectrometry). It also provides gas phase retention indices for GC. Resources include the mass spectral library, the peptide library, and a standard refernece material guide. | metabolomics, metabolomics tool, peptide, mass spectrometry, compound identification, data center, portal | is listed by: Metabolomics Workbench | https://www.nist.gov/mml/biomolecular-measurement/mass-spectrometry-data-center | SCR_014680 | Mass Spectrometry Data Center, NIST MS Data Center, MS Data Center | 2026-08-13 09:29:04 | 108 | |||||||||
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Optimouse project Resource Report Resource Website 1+ mentions |
Optimouse project (RRID:SCR_021463) | data or information resource, portal, project portal | Project related to individual mice positions analysis, specifically their nose positions. Includes software tool for analysis of mouse position data designed by Hebrew University scientists. Provides open source software to analyze positions of individual mice, specifically their nose positions, in behavioral arena with the goal of minimizing error. | Mouse position data analysis, mouse position, position data, nose position, OpenBehavior |
is listed by: OpenBehavior is related to: Optimouse has parent organization: Hebrew University of Jerusalem; Jerusalem; Israel |
DOI:10.1186/s12915-017-0377-3 | Free, Freely available | SCR_021463 | Optimouse | 2026-08-13 09:30:42 | 1 | ||||||||
|
seq-annot Resource Report Resource Website 1+ mentions |
seq-annot (RRID:SCR_018731) | software toolkit, software resource, standalone software, software application | Software Python package for annotating and counting genomic features in genomes and metagenomes. Software tools to facilitate annotation and comparison of genomes and metagenomes. | Annotating, counting, comparison, genomic feature, genome, metagenome, metagenomics, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:seq-annot | https://bio.tools/seq-annot | SCR_018731 | 2026-08-13 09:30:08 | 1 | ||||||||
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DirectOverlay Resource Report Resource Website 1+ mentions |
DirectOverlay (RRID:SCR_018978) | image analysis software, data processing software, software resource, software application | Software package for display of light microscopy images together with atomic force microscopy images. | Light microscopy, light microscopy image, atomic force microscopy, image, atomic force, microscopy | Restricted | SCR_018978 | 2026-08-13 09:30:18 | 1 | |||||||||||
|
TransDecoder Resource Report Resource Website 1000+ mentions |
TransDecoder (RRID:SCR_017647) | data processing software, software resource, standalone software, software application | Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV. | Identify, candidate, coding, region, transcript, sequence, de novo, RNAseq, assembly, alignment, genome, open, reading, frame, homology, protein, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:transDecoder, OMICS_10852 | https://bio.tools/TransDecoder, https://sources.debian.org/src/transdecoder/, https://github.com/TransDecoder/TransDecoder/wiki | SCR_017647 | , Find Coding Regions Within Transcripts | 2026-08-13 09:30:04 | 1572 | |||||||
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SpikeForrest Resource Report Resource Website 1+ mentions |
SpikeForrest (RRID:SCR_019261) | data or information resource, portal, project portal | Software reproducible, continuously updating platform which benchmarks performance of spike sorting codes across large curated database of electrophysiological recordings with ground truth. Website and open source computing framework for evaluating and comparing spike sorting algorithms for neurophysiology data analysis. Project of Center for Computational Mathematics at Flatiron Institute. | Spike sorting code performance, electrophysiological recordings, curated database, spike sorting algorithms comparing, spike sorting algorithms evaluation, neurophysiology data analysis, Flatiron Institute | Free, Freely available | SCR_019261 | 2026-08-13 09:30:37 | 2 | |||||||||||
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Smart-seq2 Single Sample Pipeline Resource Report Resource Website 1+ mentions |
Smart-seq2 Single Sample Pipeline (RRID:SCR_021228) | software toolkit, data processing software, software resource, software application | Software tool designed by Data Coordination Platform of Human Cell Atlas to process single-cell RNAseq data generated by Smart-seq2 assays.Processes stranded or unstranded, paired- or single-end, scRNA-seq data from an individual cell. | scRNAseq data, Smart-seq2 assays, processing scRNA-seq data from individual cell | has parent organization: Broad Institute | Free, Freely available | https://broadinstitute.github.io/warp/docs/Pipelines/Smart-seq2_Single_Sample_Pipeline/README | https://github.com/broadinstitute/warp/tree/master/pipelines/skylab/smartseq2_single_sample | SCR_021228 | 2026-08-13 09:30:21 | 5 | ||||||||
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QuASIMoDOH Resource Report Resource Website 1+ mentions |
QuASIMoDOH (RRID:SCR_018708) | QuASIMoDOH | image analysis software, data processing software, software resource, software application | Software tool to describe spatial patterns in degrees of inhomogeneity and to incorporate intensity based correction to analyze images with wide range of resolutions. Can be used to assess protein and lipid patterns, quantifying distribution changes and spatial reorganization at cell surface. | is a plug in for: ImageJ | Hercules foundation | PMID:27603951 | SCR_018708 | Quantitative Analysis of Spatial distributions in Images using Mosaic segmentation and Dual parameter Optimization in Histograms | 2026-08-13 09:30:27 | 1 | ||||||||
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Agilent: 4200 TapeStation System Resource Report Resource Website 50+ mentions |
Agilent: 4200 TapeStation System (RRID:SCR_018435) | instrument resource | Benchtop genetic analyzer. Electrophoresis system for DNA and RNA sample quality control. It can be used for next generation sequencing or Biobank workflow. | Benchtop Genetic Analyzer, Instrument, Equipment, Agilent, USEDit, Next Generation Sequencing, ABRF, NGS | is listed by: USEDit | https://raw.githubusercontent.com/SciCrunch/RRID-Instruments/refs/heads/main/PDF/SCR_018435.pdf | Model_Number_4200 TapeStation, , SCR_018444, SCR_019398, SCR_019395 | https://www.agilent.com/cs/library/datasheets/public/5991-6029EN.pdf | SCR_018435 | , Agilent 4200 Tapestation Genetic Analyzer, Agilent 4200 TapeStation | 2026-08-13 09:30:03 | 63 | |||||||
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Fluorescent Imaging Analysis Software FIMAS Resource Report Resource Website 1+ mentions |
Fluorescent Imaging Analysis Software FIMAS (RRID:SCR_018311) | FIMAS | image analysis software, data processing software, software resource, software application | Software tool to perform basic and specific analysis procedures on fluorescent microscopy and fluorescent lifetime imaging microscopy data. Requires MATLAB with image processing and statistical toolboxes. Can import fluorescent data from Olympus, Biorad, Femtonics, TIFF, Excel, ASCII files. | Analysis procedure, fluorescent microscopy, fluorescent imaging, microscopy data, image processing, fluorescent data | uses: MATLAB | Free, Freely available | SCR_018311 | 2026-08-13 09:30:01 | 3 | |||||||||
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mgatk Resource Report Resource Website 1+ mentions |
mgatk (RRID:SCR_021159) | software toolkit, data processing software, software resource, software application | Software python-based command line interface for processing .bam files with mitochondrial reads and generating high-quality heteroplasmy estimation from sequencing data. This package places a special emphasis on mitochondrial genotypes generated from single-cell genomics data, primarily mtscATAC-seq, but is generally applicable across other assays. | processing .bam files, mitochondrial reads, heteroplasmy estimation, sequencing data, mitochondrial genotypes, mtscATAC-seq | NCI F31 CA232670; NCI R01 CA208756; NCI P01 CA206978; NCI U10 CA180861; NIDDK R01 DK103794; NHLBI R33 HL120791 |
DOI:10.1038/s41587-020-0645-6 | Free, Available for download, Freely available | SCR_021159 | mitochondrial genome analysis toolkit | 2026-08-13 09:30:39 | 4 | ||||||||
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Behavioral Observation Research Interactive Software project Resource Report Resource Website 1+ mentions |
Behavioral Observation Research Interactive Software project (RRID:SCR_021434) | BORIS | data or information resource, portal, project portal | Project related to computer based review of previously recorded videos or live observations. Related to study of animal and human behavior. Provides open source, multiplatform standalone program that allows user specific coding environment for computer based review of previously recorded videos or live observations.Developed by scientists from University of Turin. | Specific coding environment, computer based review, previously recorded videos review, live observations review, OpenBehavior |
is listed by: OpenBehavior is related to: Behavioral Observation Research Interactive Software has parent organization: University of Turin;Turin;Italy |
DOI:10.1111/2041-210x.12584 | Free, Freely available | SCR_021434 | Behavioral Observation Research Interactive Software | 2026-08-13 09:30:30 | 9 |
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