Tools   Select Another Resource Report Type

https://github.com/ay-lab/mustache

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.

Proper citation: Mustache (RRID:SCR_026110) Copy   

•   Source: SciCrunch Registry

https://github.com/open2c/cooltools

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.

Proper citation: cooltools (RRID:SCR_026118) Copy   

•   Source: SciCrunch Registry

https://github.com/WGLab/LongReadSum

Software fast and flexible QC and signal summarization tool for long read sequencing data.

Proper citation: LongReadSum (RRID:SCR_026408) Copy   

•   Source: SciCrunch Registry

https://scvi-tools.org/

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.

Proper citation: scvi-tools (RRID:SCR_026673) Copy   

•   Source: SciCrunch Registry

https://github.com/williamslab/ped-sim

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.

Proper citation: ped-sim (RRID:SCR_026957) Copy   

•   Source: SciCrunch Registry

https://github.com/itmat/BEERS2

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.

Proper citation: BEERS2 (RRID:SCR_027287) Copy   

•   Source: SciCrunch Registry

https://github.com/RGLab/CytoML

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.

Proper citation: CytoML (RRID:SCR_027485) Copy   

•   Source: SciCrunch Registry

https://www.aideepmed.com/BioLiP/

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.

Proper citation: BioLiP (RRID:SCR_027685) Copy   

•   Source: SciCrunch Registry

https://github.com/wyang17/SQuIRE

Software RNA-seq analysis pipeline that provides quantitative and locus-specific picture of Transposable Elements expression.

Proper citation: SQuIRE (RRID:SCR_027719) Copy   

•   Source: SciCrunch Registry

https://github.com/huishenlab/biscuit

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.

Proper citation: BISCUIT (RRID:SCR_028006) Copy   

•   Source: SciCrunch Registry

https://github.com/zfyuan/EpiProfile2.0_Family

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.

Proper citation: EpiProfile (RRID:SCR_028224) Copy   

•   Source: SciCrunch Registry

https://hitaic.herokuapp.com/

Web-based application to trace tumor tissue of origin in primary and metastasized cancers.

Proper citation: HiTAIC (RRID:SCR_028181) Copy   

•   Source: SciCrunch Registry

https://github.com/lobolab/mergem/tree/v1.1.0

Software Python package and command-line tool for merging, comparing, and translating genome-scale metabolic models.

Proper citation: mergem (RRID:SCR_028616) Copy   

•   Source: SciCrunch Registry

http://nanofab.ku.edu

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.

Proper citation: University of Kansas Nanofabrication Core Facility (RRID:SCR_028756) Copy   

•   Source: SciCrunch Registry

https://aimrc.uark.edu/data-science-core/

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.

Proper citation: University of Arkansas AIMRC Data Science Core Facility (RRID:SCR_028681) Copy   

•   Source: SciCrunch Registry