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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
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ez Resource Report Resource Website 1+ mentions |
ez (RRID:SCR_020990) | data processing software, software application, data analysis software, software resource, data visualization software | Software statistical analysis R package used for easy analysis and visualization of factorial experiments. Provides interface to common analysis techniques, including analysis of variance and mixed effects modeling. Visualization functions also include design visualization for pre-analysis data auditing, and correlation matrix visualization. Package includes functions for non-parametric analysis, including permutation tests and bootstrap resampling. | Factorial experiments analysis, factorial experiments, repeated measures, correlation matrix visualization, bootstrap function, variance analysis, mixed effects modeling analysis | is listed by: CRAN | Free, Available for download, Freely available | https://github.com/mike-lawrence/ez | SCR_020990 | 2026-08-14 09:28:10 | 8 | |||||||||
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NPSV Resource Report Resource Website 1+ mentions |
NPSV (RRID:SCR_020984) | software application, simulation software, software resource | Software Python tool for standalone genotyping of deletion and insertion structural variants in short read whole genome sequencing data. Implements machine learning based approach for SV genotyping that employs NGS simulation to model the combined effects of the genomic region, sequencer and alignment pipeline. | WGS data, short read, whole genome sequencing data, standalone genotyping, insertion structural variants, deletion structural variants, structural variants, SV genotyping, NGS simulation | Free, Available for download, Freely available | SCR_020984 | Non-Parametric Structural Variant Genotyper, Non-Parametric Structural Variant genotyper | 2026-08-14 09:28:30 | 1 | ||||||||||
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SnapATAC Resource Report Resource Website 10+ mentions |
SnapATAC (RRID:SCR_020981) | software toolkit, data processing software, software application, data analysis software, software resource | Software package for analyzing scATAC-seq datasets.Used to dissects cellular heterogeneity in unbiased manner and map trajectories of cellular states. Can process data from up to million cells. Incorporates existing tools into comprehensive package for analyzing single cell ATAC-seq dataset. | scATAC-seq datasets analysis, dissects cellular heterogeneity, cellular states, map trajectories | NCI K99 CA252020; UCSD School of Medicine ; NIMH U19 MH114831 |
PMID:33637727 | Free, Available for download, Freely available | https://github.com/r3fang/SnapATAC | SCR_020981 | Single Nucleus Analysis Pipeline for ATAC-seq | 2026-08-14 09:28:18 | 23 | |||||||
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DeePhage Resource Report Resource Website 1+ mentions |
DeePhage (RRID:SCR_019243) | data processing software, software application, data analysis software, software resource, sequence analysis software | Software tool to distinguish virulent and temperate phage derived sequences in metavirome data with deep learning approach. Used to identify virome sequences as temperate phage derived or virulent phage derived fragments. | Metavirome data, identify virome sequences, derived fragment, distinguish phage derived sequences, temperate phage sequences, virulent phage sequences, deep learning | https://github.com/shufangwu/DeePhage | SCR_019243 | 2026-08-14 09:28:07 | 4 | |||||||||||
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Fruit Fly Brain Observatory Resource Report Resource Website 1+ mentions |
Fruit Fly Brain Observatory (RRID:SCR_019244) | FFBO | topical portal, data repository, data processing software, storage service resource, portal, data or information resource, software application, software resource, service resource | Open source software platform for studying fruit fly brain function, and for investigating fruit fly brain disease models that are highly relevant to mechanisms of human neurological and psychiatric disorders. Collaborative ecosystem for accelerating discovery of functional logic of fruit fly brain. Includes FlyBrainLab and BrainMapsViz. Stores and integrates fruit fly brain research data. Repository of tools and methods to build, emulate and compare fruit fly brain models in health and disease. Open framework for fruit fly brain data processing and model execution. | Fruit fly brain function, neural circuits, fly brain data, brain function data, neuron location, neuron morphology, neuron biophysical properties, genetic data, | human neurological and psychiatric disorders, Epilepsy, Parkinson | Free, Freely available | SCR_019244 | 2026-08-14 09:28:28 | 3 | |||||||||
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Omics Data Paper Generator Resource Report Resource Website 1+ mentions |
Omics Data Paper Generator (RRID:SCR_019809) | documentation generation software, workflow software, data processing software, software development tool, web service, data access protocol, software application, software resource | Software package for streamlined import of omics metadata from European Nucleotide Archive into OMICS Data Paper manuscript. Omics Data Paper R Shiny app demonstrates workflow for automatic import of ENA genomic metadata into omics data paper manuscript. Streamlined conversion of metadata into manuscript facilitates authoring of omics data papers, which allow omics dataset creators to receive credit for their work and to improve description and visibility of their datasets. | Workflow, genomics, omics, FAIR data, data paper, G Power, European Nucleotide Archive, genomic metadata, omics data paper manuscript, streamlined conversion, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: Shiny |
Horizon 2020 764840 | Free, Available for download, Freely available | biotools:omics-data-paper-shinyapp-golem | https://mdmtrv.shinyapps.io/Omics_data_paper/, https://bio.tools/omics-data-paper-shinyapp-golem | SCR_019809 | omicsdatapaper | 2026-08-14 09:28:09 | 1 | ||||||
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Waters High Definition Imaging Resource Report Resource Website 1+ mentions |
Waters High Definition Imaging (RRID:SCR_021054) | HDI | software toolkit, data processing software, software application, data analysis software, software resource | Software package contains data analysis and processing tools required for rapid and effective interrogation of imaging data. Allows for full integration of full spectrum molecular imaging experiments on SYNAPT family platforms, as well as DESI imaging on Xevo G2-XS QTof Mass Spectrometers, using single user interface. | Spectrum molecular imaging, image analysis, DESI imaging, Xevo G2-XS QTof Mass Spectrometers, SYNAPT family platforms, spectrum molecular imaging experiments | Restricted | SCR_021054 | High Definition Imaging v1.5 | 2026-08-14 09:28:31 | 1 | |||||||||
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Fluidigm CyTOF Resource Report Resource Website 10+ mentions |
Fluidigm CyTOF (RRID:SCR_021055) | data processing software, software application, data analysis software, software resource | Software for analyzing mass cytometry (CyTOF) data. | mass cytometry data analysis, CyTOF, Fluidigm, cytof | is used by: Fluidigm: CyTOF Helios Mass Cytometer | Restricted | SCR_021055 | CyTOF Software v7.0 | 2026-08-14 09:28:19 | 13 | |||||||||
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Exemplar Microscopy Images of Tissues Resource Report Resource Website 1+ mentions |
Exemplar Microscopy Images of Tissues (RRID:SCR_021052) | EMIT | image repository, data repository, experimental protocol, 2d spatial image, storage service resource, immuno detection protocol, image, data or information resource, immunofluorescence, data set, image collection, service resource, narrative resource | Reference dataset of multiplexed immunofluorescence microscopy images collected at HMS Laboratory of Systems Pharmacology. Includes set of images of different types for development and benchmarking of computational methods for image processing. As of 4/2/2021, EMIT comprises tissue microarray containing cores from 34 cancer, non-neoplastic diseases, and normal tissue collected from clinical discards under IRB supervised protocol. TMA was imaged using cyclic immunofluorescence method. Additional extensions of EMIT are currently in the planning stages. Long term goal is to compose ImageNet like resource for highly multiplexed images of tissues and tumors by consolidating high quality curated datasets. | Reference dataset, multiplexed immunofluorescence microscopy images, tissue microarray, cyclic immunofluorescence, tissues images, tumors images |
is related to: Synapse is related to: Harvard Medical School; Massachusetts; USA |
glioblastoma, lung adenocarcinoma, prostate adenocarcinoma, seminoma, meningioma, mesothelioma, GI stromal tumor, liver cirrhosis, leiomyosarcoma, high-grade serous ovarian cancer, diverticulitis, acute appendicitis, metastatic melanoma, dedifferentiated liposarcoma | NIH U54 CA225088; NCI U2C CA233262; NCI U2C CA233280; Ludwig Center at Harvard Medical School and the Ludwig Cancer Research Foundation |
DOI:10.1101/2021.03.15.435473 | Restricted | SCR_021052 | Exemplar Microscopy Images of Tissues ( and Tumors) | 2026-08-14 09:28:11 | 3 | |||||
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UnMICST Resource Report Resource Website 1+ mentions |
UnMICST (RRID:SCR_021050) | image processing software, image analysis software, data processing software, software application, software resource, segmentation software | Software tool as set of deep learning nuclei instance and semantic segmentation models that have been trained on 6 human tissue types: tonsil, small intestine, ovary, and cancers of brain, colon, prostate, and lung stained with Hoechst 33342 and combination of lamin B2 and nucleoporin98. Includes manually curated annotations as well as novel concept of introducing intentionally defocused and saturated images for robustness. | segmentation, identifying cells, segmenting tissue, universal models, tissue image, cell segmentation | Free, Available for download, Freely available | SCR_021050 | , Universal Models for Identifying Cells and Segmenting Tissue, UNet Model for Identifying Cells and Segmenting Tissue, UnMicst | 2026-08-14 09:28:19 | 3 | ||||||||||
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Autodesk Netfabb Premium Resource Report Resource Website 1+ mentions |
Autodesk Netfabb Premium (RRID:SCR_019812) | data processing software, software application, data analysis software, software resource | Software tool to open and assess stereolithographic data. Software application tailored for additive manufacturing, rapid prototyping, and 3D printing. | Assess stereolithographic data, additive manufacturing, rapid prototyping, 3D printing | Restricted | SCR_019812 | Autodesk Netfabb Premium 2019 | 2026-08-14 09:28:16 | 1 | ||||||||||
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ScanNeo Resource Report Resource Website 1+ mentions |
ScanNeo (RRID:SCR_019253) | data processing software, software application, data analysis software, software resource, sequence analysis software | Open software pipeline for analyzing RNA-seq to predict neoepitopes derived from small to large sized indels. Used for identifying indel derived neoantigens using RNA-Seq data. | RNA-Seq, neoepitopes, indel, indel derived neoantigen, RNA-Seq data, neoantigen identification | PMID:30887025 | Free, Available for download, Freely available | SCR_019253 | 2026-08-14 09:28:28 | 4 | ||||||||||
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PAM Resource Report Resource Website 1+ mentions |
PAM (RRID:SCR_020966) | data processing software, software application, data analysis software, software resource | Software package for quantitative analysis of fluorescence microscopy and spectroscopy data, with focus on experiments using pulsed interleaved excitation. Open source software package written in MATLAB that offers workflow through its graphical user interface. Framework for integrated analysis of imaging, single-molecule, and ensemble fluorescence data.Supports most types of data collection modalities. | Quantitative data analysis, fluorescence microscopy data, data analysis, spectroscopy data analysis, pulsed interleaved excitation, imaging integrated analysis |
uses: MATLAB has parent organization: Ludwig-Maximilians-University; Munich; Germany |
Deutsche Forschungsgemeinschaft ; Ludwig-Maximilians-University; Munich; Germany ; Research Foundation Flanders |
PMID:29642023 | Free, Available for download, Freely available | http://www.cup.uni-muenchen.de/pc/lamb/software/pam.html | SCR_020966 | Pulsed interleaved excitation Analysis with Matlab, Pulsed Interleaved Excitation analysis with MATLAB, PIE analysis with MATLAB | 2026-08-14 09:28:30 | 4 | ||||||
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Aperio VERSA Resource Report Resource Website 1+ mentions |
Aperio VERSA (RRID:SCR_021016) | image processing software, image analysis software, data processing software, software application, software resource | Software tool designed to support Leica Biosystems Aperio VERSA scanner. Digital pathology scanning software. Used for diverse imaging needs for digital pathology. | Leica Biosystems, Aperio VERSA scanner, digital pathology, scanning software, diverse imaging | Restricted | SCR_021016 | Aperio VERSA Digital Pathology Scanner Software | 2026-08-14 09:28:18 | 4 | ||||||||||
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igraph Resource Report Resource Website 100+ mentions |
igraph (RRID:SCR_019225) | software toolkit, data processing software, software application, data analysis software, network analysis software, network graph visualization software, software resource, data visualization software | Software package for graphs and network analysis. Provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.Can be programmed in R, Python, Mathematica, C/C Plus Plus. | Graphs analysis, network analysis, generating graph function, graph visualization |
is listed by: CRAN is listed by: SoftCite is related to: igraph for R |
Free, Available for download, Freely available | https://igraph.org/, https://github.com/igraph/igraph/releases/tag/0.8.4 | SCR_019225 | igraph 0.8.4, igraph 1.2.6 | 2026-08-14 09:28:14 | 432 | ||||||||
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Python based Relational Animal Tracking Resource Report Resource Website 1+ mentions |
Python based Relational Animal Tracking (RRID:SCR_021014) | PyRAT | software application, software resource, data management software | Software tool for management of animal facility data by Scionics Computer Innovation GmbH. Used by laboratory animal facilities. Used by researchers, animal house managers, animal keepers and others to access their data from same source. Available in English, French, German, Italian, Portuguese and Spanish. | Animal facility data, animal facility data management, Scionics Computer Innovation GmbH, | Restricted | SCR_021014 | PyRAT animal facility | 2026-08-14 09:28:11 | 1 | |||||||||
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MARS Data Analysis Software Resource Report Resource Website 10+ mentions |
MARS Data Analysis Software (RRID:SCR_021015) | data processing software, software application, data analysis software, software resource | Proprietary software package for data analysis by BMG Labtech. | Data analysis, BMG Labtech, microplate reader instrumentation software | Restricted | SCR_021015 | MARS Data Analysis, MARS | 2026-08-14 09:28:30 | 10 | ||||||||||
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epitopepredict Resource Report Resource Website 1+ mentions |
epitopepredict (RRID:SCR_019221) | software application, simulation software, software resource | Open source software tool as programmatic framework and command line tool designed to aid process of MHC binding prediction. Provides access to multiple binding prediction algorithms under single interface and scales for whole genomes using multiple target MHC alleles.Software should be run on Linux operating system. Ubuntu is recommended but most major distributions will be fine. Windows is not supported. | Protein sequence, MHC binding prediction, whole genomes, multiple target MHC allele, epitope prediction, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:epitopepredict | https://epitopepredict.readthedocs.io/en/latest/, https://bio.tools/epitopepredict | SCR_019221 | 2026-08-14 09:28:14 | 2 | ||||||||
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ABF Utility Resource Report Resource Website 1+ mentions |
ABF Utility (RRID:SCR_019222) | data processing software, software application, data analysis software, software resource | Software tool to convert data files from Mac program such as Igor and Pulse or John Dempster CDR, WinTida, to ABF formats and analyze them with Mini Analysis Program. | Convert data file, ABF format, data file, data format | Restricted | SCR_019224 | SCR_019222 | 2026-08-14 09:28:06 | 4 | ||||||||||
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OpenClinica Resource Report Resource Website 10+ mentions |
OpenClinica (RRID:SCR_019223) | data processing software, software application, software resource, data acquisition software | Web platform for electronic data capture by OpenClinica, LLC. Used as clinical trial management system. | Clinical trial, data management system, clinical trial management system, clinical data, clinical data management | is listed by: SoftCite | PMID:21893916 | Restricted | https://www.openclinica.com/community-edition-open-source-edc/ | SCR_019223 | 2026-08-14 09:28:28 | 46 |
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