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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Mustache Resource Report Resource Website 1+ mentions |
Mustache (RRID:SCR_026110) | software application, source code, software resource | Software tool for multi-scale detection of chromatin loops from Hi-C and Micro-C contact maps in high resolutions (10kbp all the way to 500bp and even more). Used to detect chromatin loops caused by interaction of DNA segments with variable size. | detect chromatin loops, interaction of DNA segments, Hi-C, Micro-C, contact maps, | NIGMS R35 GM128938 | PMID:32998764 | Free, Available for download, Freely available | SCR_026110 | Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation | 2026-07-28 09:46:32 | 5 | ||||||||
|
cooltools Resource Report Resource Website 10+ mentions |
cooltools (RRID:SCR_026118) | source code, software toolkit, software resource | Software suite of computational tools that enables flexible, scalable, and reproducible analysis of high-resolution contact frequency data. Provides suite of computational tools with paired python API and command line access, which facilitates workflows either on high-performance computing clusters or via custom analysis notebooks. As part of the Open2C ecosystem, cooltools also provides detailed introductions to key concepts in Hi-C-data analysis with interactive notebook documentation. | enables reproducible analysis, high-resolution contact frequency data, paired python API, | NIGMS R35 GM143116; NHGRI UM1 HG011536; NHGRI R01 HG003143 |
PMID:38709825 | Free, Available for download, Freely available | SCR_026118 | 2026-07-28 09:46:32 | 25 | |||||||||
|
LongReadSum Resource Report Resource Website 1+ mentions |
LongReadSum (RRID:SCR_026408) | software application, source code, software resource | Software fast and flexible QC and signal summarization tool for long read sequencing data. | signal summarization, quality control, long read sequencing data, | NHGRI F31HG013259; NHGRI HG013359; NIGMS GM132713 |
PMID:39211184 | Free, Available for download, Freely available, | SCR_026408 | 2026-07-28 09:46:38 | 1 | |||||||||
|
scvi-tools Resource Report Resource Website 10+ mentions |
scvi-tools (RRID:SCR_026673) | software application, data analysis software, source code, software resource, data processing software, software library, software toolkit | Software Python library for deep probabilistic analysis of single-cell and spatial omics data. Used for probabilistic modeling and analysis of single-cell omics data, built on top of PyTorch and AnnData. | probabilistic analysis, single-cell omics data, spatial omics data, | NIGMS R35GM124916; Chan-Zuckerberg Foundation ; NHGRI T32HG000047 |
PMID:35132262 | Free, Available for download, Freely available | https://github.com/scverse/scvi-tools | SCR_026673 | single-cell variational inference tools | 2026-07-28 09:46:44 | 31 | |||||||
|
ped-sim Resource Report Resource Website 1+ mentions |
ped-sim (RRID:SCR_026957) | software application, simulation software, source code, software resource | Software tool to simulate pedigree structures. Used for simulating relatives that can utilize either sex-specific or sex averaged genetic maps and also either model of crossover interference or traditional Poisson model for inter-crossover distances. | Pedigree simulator, simulate pedigree structures, simulating relatives, sex-specific, sex averaged, genetic maps, | NIGMS R35 GM133805; Alfred P. Sloan Research Fellowship ; United States-Israel Binational Science Foundation ; NHLBI R01 HL0113323; NHLBI P01 HL045222; NIDDK R01 DK047482; NIDDK R01 DK053889; NIGMS T32 GM007617; NIGMS T32 GM083937; Wellcome Trust |
PMID:31860654 | Free, Available for download, Freely available | SCR_026957 | Ped-sim | 2026-07-28 09:46:54 | 2 | ||||||||
|
BEERS2 Resource Report Resource Website |
BEERS2 (RRID:SCR_027287) | software application, simulation software, source code, software resource | Software for simulation of RNA-seq reads. Combines flexible and highly configurable design with detailed simulation of entire library preparation and sequencing pipeline and is designed to include effects of polyA selection and RiboZero for ribosomal depletion, hexamer priming sequence biases, GC-content biases in polymerase chain reaction (PCR) amplification, barcode read errors and errors during PCR amplification. | RNA-seq reads, simulation of RNA-seq reads, | NCATS 5UL1TR000003; NHLBI R01HL155934; NHLBI R01HL147472; NIGMS DP2GM146251 |
PMID:38605641 | Free, Available for download, Freely available | SCR_027287 | 2026-07-28 09:46:54 | 0 | |||||||||
|
CytoML Resource Report Resource Website 1+ mentions |
CytoML (RRID:SCR_027485) | source code, software toolkit, software resource | Software R package that enables cross-platform import, export, and sharing of gated cytometry data. It currently supports Cytobank, FlowJo, Diva, and R, allowing users to import gated cytometry data from commercial platforms into R. | Cross-platform cytometry data sharing, cross-platform import, export, sharing, gated cytometry data, import gated cytometry data, | NIGMS R01 GM118417; Bill and Melinda Gates Foundation ; NIAID UM1 AI068635 |
PMID:30551257 | Free, Available for download, Freely available | https://www.bioconductor.org/packages/release/bioc/html/CytoML.html | SCR_027485 | 2026-07-28 09:47:11 | 5 | ||||||||
|
BioLiP Resource Report Resource Website 100+ mentions |
BioLiP (RRID:SCR_027685) | data or information resource, database | Semi-manually curated database for biologically relevant ligand-protein binding interactions. Structure data are collected primarily from Protein Data Bank (PDB), with biological insights mined from literature and other specific databases. Database used for serving needs of ligand-protein docking, virtual ligand screening and protein function annotation.BioLiP2 offers significantly greater coverage of nucleic acid-protein interactions, and interactions involving large complexes, integrates structural alignment algorithms with structure prediction techniques, which enables composite protein structure and sequence-based searching. | curated database, ligand-protein binding interactions, ligand-protein docking, virtual ligand screening, protein function annotation, | uses: Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) | National Science Foundation ; NIGMS GM083107; NIGMS GM084222 |
PMID:23087378 PMID:37522378 |
Free, Freely available | SCR_027685 | BioLiP2 | 2026-07-28 09:47:15 | 115 | |||||||
|
SQuIRE Resource Report Resource Website 10+ mentions |
SQuIRE (RRID:SCR_027719) | SQuIRE | source code, software toolkit, software resource | Software RNA-seq analysis pipeline that provides quantitative and locus-specific picture of Transposable Elements expression. | RNA-seq analysis, quantitative and locus-specific picture of TE expression, Transposable Elements expression, | NIGMS R01GM124531; NIGMS P50GM107632 |
PMID:30624635 | Free, Available for download, Freely available | SCR_027719 | , Software for Quantifying Interspersed Repeat Expression (SQuIRE), Software for Quantifying Interspersed Repeat Expression | 2026-07-28 09:47:15 | 10 | |||||||
|
BISCUIT Resource Report Resource Website |
BISCUIT (RRID:SCR_028006) | software toolkit, software resource | Software application for simultaneous genetic and epigenetic inference in bulk and single-cell studies. Used to perform alignment, DNA methylation and mutation calling, and allele specific methylation from bisulfite sequencing data. Analyzing sodium bisulfite conversion-based DNA methylation/modification data. | simultaneous genetic and epigenetic inference, analyzing sodium bisulfite conversion-based DNA methylation/modification data, perform alignment, DNA methylation, mutation calling, allele specific methylation, bisulfite sequencing data, | NCI R37CA230748; NCI U24CA264023; NIGMS R35GM146978 |
PMID:38412294 | Free, Available for download, Freely available | SCR_028006 | , BISulfite-seq CUI Toolkit, BISulfite-seq CUI Toolkit (BISCUIT) | 2026-07-28 09:47:19 | 0 | ||||||||
|
EpiProfile Resource Report Resource Website |
EpiProfile (RRID:SCR_028224) | software application, source code, software resource | Software tool for processing Epi-Proteomics mass spectrometry data. Discriminates isobaric histone peptides using distinguishing fragment ions in their tandem mass spectra and extracts the chromatographic area under the curve using previous knowledge about peptide retention time. Nanoflow liquid chromatography coupled with high resolution tandem mass spectrometry-based quantification tool for histone peptides, which can also be adapted to analyze nonhistone protein samples. EpiProfile 2.0 is extended version of v1.0 for enhanced quantification of histone peptides based on LC-MS/MS analysis. | LC-MS/MS analysis, peptide, quantification, histone, quantification of histone peptides, quantification of histone peptides based on LC-MS/MS analysis, mass spectrometry data, | NIGMS GM110174; NIAID AI118891; NCI CA196539; UPenn Epigenetics Institute ; NCATS TL1TR001880; NIGMS T32GM008275 |
PMID:25805797 PMID:29790754 |
Free, Available for download, Freely available | SCR_028224 | EpiProfile 2.0 | 2026-07-28 09:47:21 | 0 | ||||||||
|
HiTAIC Resource Report Resource Website |
HiTAIC (RRID:SCR_028181) | software resource, data access protocol, web service | Web-based application to trace tumor tissue of origin in primary and metastasized cancers. | Tumor classifier, trace tumor tissue of origin, primary and metastasized cancers, | NIGMS P20GM104416; NCI R01CA253976; NCI R01CA216265; NCI R01CA275974; NCI P30CA023108 |
PMID:37089814 | Free, Freely available | SCR_028181 | Hierarchical Tumor Artificial Intelligence Classifier | 2026-07-28 09:47:08 | 0 | ||||||||
|
mergem Resource Report Resource Website |
mergem (RRID:SCR_028616) | software toolkit, software resource | Software Python package and command-line tool for merging, comparing, and translating genome-scale metabolic models. | merging, comparing, translating, genome-scale metabolic models, | is organization facet of: University of Maryland; Maryland; USA | NIGMS R35GM137953 | PMID:38312936 | Free, Available for download, Freely available | https://zenodo.org/records/10740987 | SCR_028616 | 2026-07-28 09:47:20 | 0 | |||||||
|
University of Kansas Nanofabrication Core Facility Resource Report Resource Website |
University of Kansas Nanofabrication Core Facility (RRID:SCR_028756) | access service resource, service resource, core facility | Provides manufacturing micro- and nanofluidic devices for biomedical research, equipment and resources for applications with micro- and nanofabrication needs. Facility conisists of ISO class 7 cleanroom space, housing tools and materials for techniques including photolithography, nano-imprint lithography, plasma (dry) etching (ICP-RIE), wet etching, thin film deposition, scanning electron microscopy (VP-SEM), atomic force microscopy, contact angle goniometry, ellipsometry, profilometry, wafer dicing, wire bonding, laser ablation and engraving, 3D printing, hot embossing, and COMSOL software for device modeling. In addition, the facility has numerous microscopes for general inspection, ovens and furnaces, ultrapure water, and dedicated process fume hoods. | ABRF, nanofabrication cleanroom facility, biomedical research device, device manufacturing, |
is listed by: ABRF CoreMarketplace has parent organization: University of Kansas; Kansas; USA |
NIGMS P30GM145499 | Restricted | ABRF_6056 | https://coremarketplace.org/?FacilityID=6056&citation=1 | SCR_028756 | University of Kansas Nanofabrication Facility (KUNF) | 2026-07-28 09:47:25 | 0 | ||||||
|
University of Arkansas AIMRC Data Science Core Facility Resource Report Resource Website |
University of Arkansas AIMRC Data Science Core Facility (RRID:SCR_028681) | access service resource, service resource, core facility | Core specializes in artificial intelligence-based approaches to elucidate relationships between large imaging, bioenergetics, genomic, and proteomic data sets. Provided services include: 1) foundational training for those getting started with high-performance computing and Arkansas Research Platform (ARP), 2) training and support for the collaborative use of a 508 TB data storage server exclusively maintained for and catering to AIMRC researchers, 3) training for Python programming, basic data mining, and machine learning, 4) training and support for using open-source deep learning based biomedical imaging resources (e.g., ZeroCostDL4Mic and Bioimage Model Zoo), and 5) customized solutions for deep learning based and large foundational models based biomedical imaging analysis, multi-omics data integration and analysis, and quantitative analysis pipelines for large data sets. | ABRF, Center of Biomedical Research Excellence (COBRE), data science services, large imaging, bioenergetics, genomic, proteomic, data sets, |
is listed by: ABRF CoreMarketplace has parent organization: University of Arkansas; Arkansas; USA |
NIGMS P20GM139768 | ABRF_6033 | https://coremarketplace.org/RRID:SCR_028681/?citation=1 | SCR_028681 | , Arkansas Integrative Metabolic Center (AIMRC) Data Science Core | 2026-07-28 09:47:25 | 0 |
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