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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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GeoPandas Resource Report Resource Website 10+ mentions |
GeoPandas (RRID:SCR_028590) | software toolkit, software resource, software library | Software open-source Python library that makes it easy to work with geospatial data. It extends the popular data analysis library, Pandas, by allowing you to perform spatial operations on geometric shapes like points, lines, and polygons. | Python, geographic data, perform spatial operations on geometric shapes, | Free, Available for download, Freely available | https://github.com/geopandas/geopandas | SCR_028590 | 2026-08-15 11:33:17 | 18 | ||||||||||
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pip Resource Report Resource Website 1+ mentions |
pip (RRID:SCR_028591) | software toolkit, source code, software resource | Software package installer for Python. You can use pip to install packages from the Python Package Index and other indexes. | Python package installer, | Free, Available for download, Freely available | https://github.com/pypa/pip | SCR_028591 | 2026-08-15 11:33:17 | 1 | ||||||||||
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mhcflurry Resource Report Resource Website 1+ mentions |
mhcflurry (RRID:SCR_028577) | software toolkit, source code, software resource | Software MHC I ligand prediction package with competitive accuracy and documented implementation. Used for peptide-MHC I binding affinity prediction. | MHC I ligand prediction, peptide-MHC I binding affinity prediction, peptide-MHC I, binding affinity prediction, | Free, Available for download, Freely available | SCR_028577 | 2026-08-15 11:33:24 | 2 | |||||||||||
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ASCAT sc Resource Report Resource Website 1+ mentions |
ASCAT sc (RRID:SCR_028613) | source code, software application, software resource | Software application as implementation of ASCAT allowing generation of CNV profiles from single cell and short coverage sequencing data. | generation of CNV profiles, single cell, short coverage sequencing data, | Free, Available for download, Freely available | SCR_028613 | 2026-08-15 11:33:23 | 1 | |||||||||||
|
CINSignatureQuantification Resource Report Resource Website 1+ mentions |
CINSignatureQuantification (RRID:SCR_028614) | software toolkit, source code, software resource | Software R package to quantify the activity of signatures of chromosomal instability from absolute copy number profiles. Used to quantifying copy number signatures from absolute copy number profiles. | Quantifying copy number signatures, absolute copy number profiles, signatures of chromosomal instability, | Free, Available for download, Freely available | SCR_028614 | 2026-08-15 11:33:18 | 4 | |||||||||||
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PANGEA Resource Report Resource Website 1+ mentions |
PANGEA (RRID:SCR_028559) | data or information resource, atlas | Spacial neuron gene expression atlas. Interactive, server-free web application and spatial transcriptomics database designed to help researchers map and analyze gene expression within the brain. Mouse whole brain spatial transcriptomic atlas. | Spacial neuron gene expression atlas, mice, neuronal gene expression from wild type mice, spatial transcriptomics, gene expression within brain, | PMID:39484617 | Free, Freely available | SCR_028559 | sPAtial Neuronal Gene Expression Atlas | 2026-08-15 11:33:23 | 6 | |||||||||
|
BeAtMuSiC Resource Report Resource Website 1+ mentions |
BeAtMuSiC (RRID:SCR_028562) | data access protocol, software resource, web service | Web tool for prediction of changes in protein-protein binding affinity on mutations. Predictor of changes in binding free energy induced by point mutations. It relies on a set of statistical potentials derived from known protein structures, and combines the effect of the mutation on the strength of the interactions at the interface, and on the overall stability of the complex. | prediction of changes in protein-protein binding affinity, mutations, changes in binding free energy, point mutations, | Belgian Fund for Scientific Research | PMID:23723246 | Free, Freely available | SCR_028562 | 2026-08-15 11:33:22 | 3 | |||||||||
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Mississippi State University; Mississippi; USA Resource Report Resource Website 1+ mentions |
Mississippi State University; Mississippi; USA (RRID:SCR_000361) | university | Public university in Mississippi with land, sea and space grants that offers degree programs in areas such as agriculture and applied sciences at the undergraduate and graduate levels. | mississippi, land, sea, space, grant, agriculture, applied science |
is parent organization of: Chicken Gene Nomenclature Consortium is parent organization of: AgBase is parent organization of: Bovine Gene Atlas is parent organization of: Corn Fungal Resistance Associated Sequences Database is parent organization of: Bird Base is parent organization of: Mississippi State University Institute for Imaging and Analytical Technologies I2AT Core Facility |
Wikidata Q1939211, GRID grid.260120.7, nlx_23152, ISNI 0000 0001 0816 8287, Crossref Funder ID 100007250 | https://ror.org/0432jq872 | SCR_000361 | 2026-08-15 11:21:48 | 1 | |||||||||
|
TAPS Resource Report Resource Website 1+ mentions |
TAPS (RRID:SCR_000356) | software resource | A bioinformatic tool for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays. | standalone software, affymetrix |
is listed by: OMICtools has parent organization: Google Code |
PMID:22023820 | OMICS_02571 | SCR_000356 | Tumor Aberration Prediction Suite | 2026-08-15 11:21:43 | 2 | ||||||||
|
University of Sydney; Sydney; Australia Resource Report Resource Website 1+ mentions |
University of Sydney; Sydney; Australia (RRID:SCR_000381) | university | A public research university in Sydney, Australia that offers a wide range of degree programs at the undergraduate and graduate level. | public, research, university, sydney, australia, training service resource |
uses: LabArchives is related to: International AMD Genetics Consortium is related to: LabArchives is parent organization of: Using our Brains Tissue Donor Program is parent organization of: Australian New Zealand Clinical Trials Registry is parent organization of: MF-GE is parent organization of: OMIA - Online Mendelian Inheritance in Animals is parent organization of: Australian Microscopy and Microanalysis Research Facility is parent organization of: CiteFuse |
ISNI:0000 0004 1936 834X, nlx_143763, grid.1013.3, Crossref funder ID:501100001774, Wikidata:Q487556 | https://ror.org/0384j8v12 | SCR_000381 | University of Sydney | 2026-08-15 11:21:49 | 1 | ||||||||
|
is-rSNP Resource Report Resource Website 1+ mentions |
is-rSNP (RRID:SCR_000387) | is-rSNP | software resource | Software tool that predicts whether a single nucleotide polymorphism (SNP) is a regulatory SNP (rSNP). For a given SNP, and using a statistical framework, it can successfully predict the set of transcription factors (TFs) for which binding is affected. The algorithm provides the statistical power to scan large numbers of SNPs, making it suitable to use to screen all associated SNPs output by a typical genome-wide association studies (GWAS). | genome-wide association study, single nucleotide polymorphism, transcription factor, regulatory single nucleotide polymorphism, in silico |
is listed by: OMICtools has parent organization: University of Melbourne; Victoria; Australia |
PMID:20823317 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01930 | SCR_000387 | In silico regulatory SNP detection, is-rSNP: in silico regulatory SNP detection | 2026-08-15 11:21:44 | 1 | ||||||
|
AS-Peak Resource Report Resource Website 1+ mentions |
AS-Peak (RRID:SCR_000380) | ASPeak | software resource | A software that utilizes a peak detection algorithm to identify RNA-protein binding sites. | rna, peak detection, protein, binding, site, algorithm, analysis |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23929032 | Free, Available for download, Freely available | OMICS_00566 | https://omictools.com/aspeak-tool | SCR_000380 | 2026-08-15 11:21:44 | 2 | ||||||
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GENSENG Resource Report Resource Website 1+ mentions |
GENSENG (RRID:SCR_000378) | data processing software, software application, data analysis software, software resource | Software for detecting copy number variations from next generation sequencing data. Used to identify regions of discrete copy number changes while simultaneously accounting for effects of multiple confounders. | next generation sequencing data, detecting copy number variations, discrete copy number changes, identify regions |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23275535 | Free, Available for download, Freely available | OMICS_00345 | SCR_000378 | 2026-08-15 11:21:49 | 1 | ||||||||
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flowFlowJo Resource Report Resource Website 10+ mentions |
flowFlowJo (RRID:SCR_000410) | software resource | A Bioconductor package that can import gates defined by the commercial package FlowJo and work with them in a manner consistent with the other flow packages in Bioconductor. FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the FlowJo Workspace. This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm. | software package, mac os x, unix/linux, windows, r, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:19956421 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_05598 | SCR_000410 | flowFlowJo - Tools for extracting information from a FlowJo workspace and working with the data in the flowCore paradigm | 2026-08-15 11:21:50 | 21 | |||||||
|
University of Texas at Dallas; Texas; USA Resource Report Resource Website 1+ mentions |
University of Texas at Dallas; Texas; USA (RRID:SCR_000375) | UTD | university | A public research university in Texas that offers degree programs in engineering, business, political science and the natural sciences at the undergraduate and graduate levels. The university also houses research that focuses on space science, bioengineering, cybersecurity, nanotechnology, and behavioral and brain sciences. | public, research, engineering, political science, natural science, business, space science, bioengineering, cybersecurity, nanotechnology, behavioral, brain sciences, neuroscience, psychology |
has parent organization: University of Texas System; Texas; USA is parent organization of: DOMINE: Database of Protein Interactions is parent organization of: University of Texas at Dallas School of Behavioral and Brain Sciences is parent organization of: ExPosition Packages is parent organization of: MB-GAN is parent organization of: University of Texas at Dallas UTD Genome Center Core Facility is parent organization of: University of Texas at Dallas UTD Imaging and Histology Core Facility |
grid.267323.1, nlx_11355, ISNI:0000 0001 2151 7939, Wikidata:Q1781394 | https://ror.org/049emcs32 | SCR_000375 | 2026-08-15 11:21:49 | 1 | ||||||||
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BD Biosciences: FACSCalibur Flow Cytometry System Resource Report Resource Website 100+ mentions |
BD Biosciences: FACSCalibur Flow Cytometry System (RRID:SCR_000401) | BD FACSCalibur system | instrument resource | Automated benchtop flow cytometry system. It allows measuring four fluorochrome-conjugates, forward and side scatter., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | flow cytometry, hardware, instrument, equipment | has parent organization: BD Biosciences | THIS RESOURCE IS NO LONGER IN SERVICE | https://drive.google.com/file/d/1v6yeGl7IxHS0_Ezn35dZ9qzu27jIBh52/view?usp=drivesdk | SciRes_000153 | https://www.bdbiosciences.com/content/dam/bdb/marketing-documents/BD_FACSCalibur_instructions.pdf | SCR_000401 | FACSCalibur flow cytometer | 2026-08-15 11:21:44 | 411 | |||||
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Opal Research Resource Report Resource Website 1+ mentions |
Opal Research (RRID:SCR_000405) | data processing software, software application, data analysis software, software resource, sequence analysis software | Software which integrates a comprehensive, automated genome annotation engine with the VAAST and Phevor disease gene prioritization tools to rank gene variants on the severity of their impact on protein function and likelihood to cause disease. Each variant in a gene is analyzed for its impact on protein function, conservation and frequency. Each gene is ranked rather than filtered in order to ensure critical targets are not prematurely removed. | sequence analysis software, genome interpretation, variant prioritization, disease gene prioritization, next-generation sequencing, clinical interpretation, clinical genomics software, genome, protein function, disease, genomic variant, mutation | is related to: VAAST | PMID:23895124 | Restricted | SciRes_000140 | SCR_000405 | Omicia Opal Research, Omicia Opal, Opal Research Variant Interpretation | 2026-08-15 11:21:50 | 1 | |||||||
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Lasergene's SeqMan Pro Resource Report Resource Website 1+ mentions |
Lasergene's SeqMan Pro (RRID:SCR_000283) | data processing software, software application, data analysis software, software resource, data visualization software | Software for analysis and DNA sequence assembly of Sanger data. It also provides visualizations and analysis of next-gen projects assembled by SeqMan NGen. | dna, sequence, analysis, sanger, snp discovery, data visualization |
is listed by: OMICtools works with: GenVision |
Restricted | OMICS_01810 | SCR_000283 | Lasergenes SeqMan Pro, SeqMan Pro, SeqMan Pro - Software for Contig Assembly and Analysis Including SNP Discovery Coverage Evaluation and Project Annotation, DANSEUR Lasergenes SeqMan Pro | 2026-08-15 11:21:42 | 5 | ||||||||
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IrfanView Resource Report Resource Website 10+ mentions |
IrfanView (RRID:SCR_000315) | software resource | An open source graphic viewer. Some features include batch conversion, paint options, basic editing and several supported file formats. It is compatible with Windows 9x, ME, NT, 2000, XP, 2003 , 2008, Vista, Windows 7, Windows 8, and Windows 10. | graphic viewer, open source, windows | Free, Available for download, Freely available | nlx_157659 | SCR_000315 | 2026-08-15 11:21:43 | 13 | ||||||||||
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flowStats Resource Report Resource Website 1+ mentions |
flowStats (RRID:SCR_000399) | software resource | Software using statistical methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the flowCore package. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05611 | SCR_000399 | flowStats - Statistical methods for the analysis of flow cytometry data | 2026-08-15 11:21:44 | 1 |
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