Curator Dashboard

Provides full-service consultation, sample processing and results. After running your samples, we will process your data using Mestranova and give you access to the raw data via email or Dropbox.

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• 11 months ago - submitted by Edyta Vieth

Core provides training, education, statistics and data management services. Services include: experimental design of new studies, advising on outcomes selection, determining or justifying sample size, designing randomization schemes,designing and writing the statistical analysis/modeling section(s), advising on appropriate database design and implementation methods, advising on the use of national data registries, health system data, grant writing on relevant sections within our specialties, creating custom databases and data entry portals for prospective studies, creating custom datasets or extracts from existing data sources for analysis, merging complex or multi-sourced data in concert with research aims and objectives, implementing blind, double-blind and other randomization schemes and more.

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• 11 months ago - submitted by Edyta Vieth

Software R package to access and explore existing scRNA-seq data from various public repositories. Supports downloading scRNA-seq data types, including raw data (SRA and ENA), count matrices (GEO, UCSC Cell Browser, and PanglaoDB), and processed objects (Zenodo, CELLxGENE, and HCA). Can access and explore existing scRNA-seq data, load output/downloaded count matrices and annotations to R (SeuratObject/DESeqDataSet), extract a subset of the SeuratObject based on cell metadata and genes, and merge multiple SeuratObjects if applicable. Provides format conversions between different scRNA-seq objects, including SeuratObject, AnnData, SingleCellExperiment, CellDataSet/cell_data_set, and loom.

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• 11 months ago - submitted by Yabing Song

Software tools for working with scATAC-seq fragment files.

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• 11 months ago - submitted by Seppe De Winter

Software R package for tidying output of statistical models.

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• 11 months ago - by Anonymous

GEfetch2R is an R package dedicated to facilitating researchers to access and explore existing scRNA-seq data from various public repositories. As a data downloader, GEfetch2R supports downloading the most diverse scRNA-seq data types, including raw data (SRA and ENA), count matrices (GEO, UCSC Cell Browser, and PanglaoDB), and processed objects (Zenodo, CELLxGENE, and HCA). Besides the data download ability, GEfetch2R can process the downloaded data, load output/downloaded count matrices and annotations to R (SeuratObject/DESeqDataSet), extract a subset of the SeuratObject based on cell metadata and genes, and merge multiple SeuratObjects if applicable. Furthermore, to enable the integration of scRNA-seq data and the interoperability between different analysis tools, GEfetch2R provides the most comprehensive format conversions between different scRNA-seq objects, including SeuratObject, AnnData, SingleCellExperiment, CellDataSet/cell_data_set, and loom. In particular, GEfetch2R benchmarks the format conversion tools for converting between SeuratObject/SingleCellExperiment and AnnData. In addition to fetching scRNA-seq data, GEfetch2R can also be used to download raw data (SRA and ENA) and count matrices (GEO) of bulk RNA-seq, process the downloaded data, and load output/downloaded count matrices to R (DESeqDataSet).

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• 11 months ago - submitted by Yabing Song

Portal provides information, guidelines, data, services, and other resources aimed at supporting the research community in the Netherlands to share data related to pathogens and pandemic preparedness.

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• 11 months ago - by Anonymous

Software tool as lite implementation of tfmodisco, a motif discovery algorithm for genomics experiments. Rewrite of the original TF-MoDISCo code.

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• 11 months ago - submitted by Seppe De Winter

Software Java-based package for statistical natural language processing, document classification, clustering, topic modeling, information extraction, and other machine learning applications to text.

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• 11 months ago - submitted by Seppe De Winter

Software suite of population scale analysis tools for single-cell genomics data.

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• 11 months ago - submitted by Seppe De Winter

Core brings together expertise from across MSU to support research through advanced omics data analysis, grant proposal assistance, and tailored training for researchers at all career stages.

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• SciCrunch
• 11 months ago - submitted by Edyta Vieth

Software repository provides optimization algorithms applied to Jarvis3 genomic compressor used for compression of genomic sequences.

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• 11 months ago - by Anonymous

Software R tool for enumerating immune cell subsets from whole tumor tissue samples. Utilizes adaptive least trimmed square to automatically detect and remove outliers before estimating cell compositions.

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• 11 months ago - by Anonymous

Software ensembl based annotation R package. Exposes annotation databases generated from Ensembl. This package loads SQL connection to database containing annotations from Ensembl.

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• 11 months ago - by Anonymous

Software Python package to build gene regulatory networks using combined or separate single-cell gene expression and single-cell chromatin accessibility (scATAC-seq) data. Used for inferring and analyzing enhancer-driven gene regulatory networks using single-cell multiomic data.

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• 11 months ago - by Anonymous

Core provides access to expertise and instrumentation for bioanalytical assay development and quantitative sample analysis, experimental design, data analysis and modeling applied in pre-clinical and clinical research involving development of novel therapies for cancer treatment and prevention, chemopreventive or carcinogenic components in food/environmental sources, and biomarkers relevant to drug therapy, nutrients, food products, and dietary patterns.

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• 11 months ago - by Anonymous

BRAIN Initiative data archive for multi-modal neurophysiological and behavioral data, supporting the Brain Behavior Quantification and Synchronization (BBQS) Program. Accessible and versatile data archive for storage, processing, and curation of multimodal neurophysiological and behavioral datasets. EMBER extends established BRAIN Initiative data infrastructure, provides new data harmonization and synchronization capabilities, and supports scalable integrations for data coordination and AI driven batch processing to enable the goals of the BBQS program.

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• 11 months ago - submitted by Brock Wester

Core assists in evaluating disease and its cure within complete biological system. Combines expertise and instrumentation to assist investigations on the mechanisms of disease development, to enable the evaluations of drug efficacy and resistance, and to provide the means for testing novel strategies and devices for disease detection and drug delivery.

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• SciCrunch
• 11 months ago - submitted by Edyta Vieth

Software application to prepare figures for publication in reproducible way. This means you receive a figure representing your data and alongside a generated code file that can exactly reproduce the figure as you put them in the publication, without the need to readjust things in external programs. Offers interactive interface to find the best way to present your data in a figure for publication. Added formatting an styling can be saved by automatically generated code. To compose multiple figures to panels, pylustrator can compose different subfigures to a single figure.

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• 11 months ago - by Anonymous

Flow Cytometry Core provides instrumentation, expertise and services. Samples are prepared by individual investigators, who then deliver to the Core for flow cytometric analysis or cell sorting. The Core also provides assistance in grant and publication preparation, publication-quality graphics, and the development of experimental designs.

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• 11 months ago - by Anonymous