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https://github.com/JLSteenwyk/ClipKIT

Software fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others. Multiple sequence alignment-trimming algorithm for accurate phylogenomic inference.

Proper citation: ClipKIT (RRID:SCR_026411) Copy   

•   Source: SciCrunch Registry

https://www.seattlechildrens.org/research/resources/behavioral-phenotyping-core/

Core dedicated to the protocol driven collection, analysis, and reporting of behavioral data using a blend of classic and innovative assays. Supports neuroscience, psychology, pharmacology, genetics, cancer, and development by providing advanced tools and expertise for the precise measurement and interpretation of behavior.

Proper citation: Seattle Childrens Research Institute Behavioral Phenotyping Core Facility (RRID:SCR_026371) Copy   

•   Source: SciCrunch Registry

https://github.com/melobio/Attune

Software framework for integrating gene expression and chromatin accessibility, enabling the inference of regulatory mechanisms and the prediction of gene expression from cross-modal data. Repository contains code and tutorials for the following tasks: multimodal pretraining, cross-modal prediction, inferring regulatory network and potential analysis.

Proper citation: Attune (RRID:SCR_026494) Copy   

•   Source: SciCrunch Registry

https://tibble.tidyverse.org/

Software package for modern re-imagining of data frame. Provides 'tbl_df' class with stricter checking and better formatting than traditional data frame.

Proper citation: tibble (RRID:SCR_026493) Copy   

•   Source: SciCrunch Registry

https://www.research.uky.edu/light-microscopy-core

Core facility offers fluorescence, confocal, super resolution, multi-photon, laser capture and atomic force microscopy. Provides central preparatory laboratory and high-end computer workstations for data analysis and image processing. Technical support ranges from investigator training on instrumentation, allowing independent use, to complete processing of samples and final imaging by facility staff. The facility is GRP accredited, undergoes annual compliance checks and provides extensive standard operating procedures for all instrumentation.

Proper citation: University of Kentucky Light Microscopy Core Facility (RRID:SCR_026405) Copy   

•   Source: SciCrunch Registry

https://touchstonelabs.org/metabolic-phenotyping-core

Academic core facility provides analytical and phenotypical measures to the scientific community. Provides services related to metabolic disorders (diabetes and obesity), cancer, aging neurological disorders, etc. Provides letters of support for grant proposals and research applications.

Proper citation: University of Texas Southwestern Medical Center Dallas Metabolic Phenotyping Core Facility (RRID:SCR_026404) Copy   

•   Source: SciCrunch Registry

https://igit.informatik.htw-dresden.de/aagef650/spheroidsegdedeb

Software minimal tool for segmentation of irradiated tumor spheroids using optimized U-Net.

Proper citation: SpheroidSegDeDeb (RRID:SCR_026409) Copy   

•   Source: SciCrunch Registry

https://www.icds.psu.edu/roar-collab/

Provides advanced cyberinfrastructure resources including large scale compute and data storage. to the Penn State University research community under the operation of the Institute of Computational and Data Sciences

Proper citation: Penn State Institute of Computational and Data Sciences Roar Core Facility (RRID:SCR_026424) Copy   

•   Source: SciCrunch Registry

https://nuance.northwestern.edu/facilities/spid/index.html

SPID provides imaging instrumentation and support facilities for atomic to molecular imaging. Supports broad range of nanoscale science and technology characterization needs at nanoscale by providing resources coupled with expert staff. Research at SPID encompasses physical and chemical sciences, engineering and life sciences, and has a strong inter-disciplinary emphasis.

Proper citation: Northwestern University NUANCE SPID Core Facility (RRID:SCR_026380) Copy   

•   Source: SciCrunch Registry

https://github.com/kharchenkolab/conos

Software R package for joint analysis of multiple single-cell RNA-seq datasets. Used to wire together large collections of single-cell RNA-seq datasets, which allows for both identification of recurrent cell clusters and propagation of information between datasets in multi-sample or atlas-scale collections.

Proper citation: Conos (RRID:SCR_026381) Copy   

•   Source: SciCrunch Registry

https://www.research.uky.edu/magnetic-resonance-imaging-and-spectroscopy-center

Service and consultation core supporting basic and clinical research. Provides advanced 3T Siemens PRISMA scanner with high performance gradients, echo-planar whole body imaging and hydrogen spectroscopic capabilities for both human and animal studies. For dedicated animal studies Bruker/Siemens 7T MR scanner has been installed.

Proper citation: University of Kentucky Magnetic Resonance Imaging and Spectroscopy Center Core Facility (RRID:SCR_026383) Copy   

•   Source: SciCrunch Registry

https://github.com/ZhantianXu/PISAD

Software reference-free intraspecies sample anomalies detetion tool based on k-mer counting.

Proper citation: PISAD (RRID:SCR_026597) Copy   

•   Source: SciCrunch Registry

https://github.com/mawenlong2016/DeepAnnotation

Software Python package to perform genomic selection. Predicts phenotypes from comprehensive multi-omics functional annotations with interpretable deep learning framework. Novel interpretable DL-based genomic prediction model that integrates comprehensive species- and tissue-level transcriptional regulatory functional annotations to predict phenotypes.

Proper citation: DeepAnnotation (RRID:SCR_026630) Copy   

•   Source: SciCrunch Registry

https://www.txgen.tamu.edu/

Core provides services including Sequencing, Library preparation, Bioinformatics Analysis and Processing. Experienced staff provide expertise to users.

Proper citation: Texas A and M University System Genomics and Bioinformatics Service Core Facility (RRID:SCR_026632) Copy   

•   Source: SciCrunch Registry

https://www.fredhutch.org/en/research/divisions/public-health-sciences-division/research/prevention-center.html

Provides services in the conduct of exercise interventions, nutrition interventions, or prevention-based clinical interventions. Facility offers well-trained, specialized staff and inviting space for study participants to participate in population-based research.

Proper citation: Fred Hutchinson Cancer Center Prevention Center Shared Resource Core Facility (RRID:SCR_026631) Copy   

•   Source: SciCrunch Registry

https://github.com/ddarriba/modeltest

Software tool for selecting the best-fit model of evolution for DNA and protein alignments. Used for selection of DNA and Protein evolutionary models.

Proper citation: modeltest (RRID:SCR_026633) Copy   

•   Source: SciCrunch Registry

https://www.augusta.edu/cancer/research/shared-resources/immune-monitoring/

Core provides services in Assay Development, Assays Experimental Design, Immune Monitoring, Cytokine Assays, ELISA, multiplex Flow based and Luminex based Bead Arrays, Project Based Flow Cytometry and Data Analysis.

Proper citation: Augusta University Georgia Cancer Center Immune Monitoring Shared Resource Core Facility (RRID:SCR_026590) Copy   

•   Source: SciCrunch Registry

https://github.com/Neural-Systems-at-UIO/CreateZoom/tree/main

Backend application to process high-resolution histology images to DeepZoomImage format, made of smaller tiles, for use in the QUINT Workflow.

Proper citation: CreateZoom (RRID:SCR_026625) Copy   

•   Source: SciCrunch Registry

https://github.com/aertslab/PUMATAC

Software pipeline for universal mapping of ATAC-seq.

Proper citation: PUMATAC (RRID:SCR_026624) Copy   

•   Source: SciCrunch Registry

https://github.com/buenrostrolab/scPrinter

Softwre framework for multi-scale footprinting analysis of single-cell ATAC-seq data. Designed to identify and visualize regulatory elements that drive cell-type-specific gene expression programs through footprinting. Uses deep learning model to predict activity of transcription factors from single-cell ATAC-seq data. Provides suite of visualization tools to explore calculated multi-scale footprints.

Proper citation: scPrinter (RRID:SCR_026644) Copy   

•   Source: SciCrunch Registry