Curator Dashboard

Viewer for DNA Methylation Atlas of Mouse Brain at Single Cell Resolution. Browser to interactively explore single cell methylome dataset including exploration of methylation diversity of one gene at single-cell or cell-type level, exploration of cell type composition of adult mouse brain dissection regions and anatomical structures, explorartion of spatial distribution and methylation signature genes of one cell type.

• Resource
• NIF
• 6 years ago - submitted by Maryann Martone

Portal for scRNA-seq study. Includes dendrogram visualization and clustering of all cells in scRNA-seq study as well as interactive filtered views for cell type, gene and/or donor group.

• Resource
• RRID-Legacy
• 6 years ago - submitted by Anh Nguyet Vu

Software tool to enable BLAST to identify homologous gene sequences. Graph based algorithm, which automatically filters High Scoring Pairs into well defined groups, each representing candidate gene in target genome.Used for identifying homologous sequences. Used for extracting relevant HSPs that represent candidate homologous genes from the entire HSP report.

• Resource
• RRID-Legacy
• 6 years ago - by Anonymous

Software package for DNA methylation analysis. Used for context-wise, gene-wise, bin-wise, region-wise and sample-wise analysis and visualizations. Used to improve precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data.

• Resource
• RRID-Legacy
• 6 years ago - by Anonymous

Software tool as simulation framework for testing association of genomic intervals. Used for estimating significance of overlap between multiple sets of genomic intervals. Estimates statistical significance based on simulation and controls for multiple tests using false discovery rate.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software tool as versatile aligning pipeline for bisulfite sequencing data. Used for mapping bisulfite sequencing data and generating DNA methylomes. Improves mappability over existing aligners by using local alignment. Maps reads from RRBS library by building special indexes with improved efficiency and accuracy. Provides additional function for filtering out reads with incomplete bisulfite conversion, which is useful in minimizing overestimation of DNA methylation levels.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software package for analysing small RNA data. Software suite of tools for analyzing miRNAs and sRNAs. Performs analysis of single or multiple sample small RNA datasets from both plants and animals.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software pipeline to identify MITEs as well as other small Class 2 non autonomous Transposable Elements from genomic DNA data sets. Used for discovering miniature inverted repeat transposable elements from genomic sequences. Can search large genomic data sets including whole genome sequences.

• Resource
• RRID-Legacy
• 6 years ago - by Anonymous

Automated software resource that combines histologically cleared volumes with connectivity atlases and MRI, enabling analysis of histological features across multiple fiber tracts and networks, and their correlation with in vivo biomarkers.Multimodal image registration and connectivity analysis for integration of connectomic data from microscopy to MRI. Open source pipeline for automated registration of mice clarity data to Allen reference atlas, segmentation and feature extraction of mice clarity data in 3D, registration of mice multimodal imaging data to Allen reference atlas, tract or label specific connectivity analysis based on Allen connectivity atlas,comparison of diffusion tensort imaging/tractography, virus tracing using CLARITY and Allen connectivity atlas, statistical analysis of CLARITY and Imaging data, atlas generation and label manipulation.

• Resource
• dkNET
• 6 years ago - submitted by Maryann Martone

Software provides user interface for data acquisition on MACSQuant Analyzer Flow Cytometer Instrument and also works as stand alone application for flow cytometry data analysis.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software tool for flow cytometry data analysis by Miltenyi Biotec.

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• RRID-Legacy
• 6 years ago - by Anonymous

Free cloud platform for secure neuroscience data analysis. Allows to manage data, processing and results, sharing projects privately with collaborators or publicly with brainlife.io community.Promotes engagement and education in reproducible neuroscience.You can share your neuroimaging data publicly or privately. Data on brainlife.io is organized as Datatypes to allow interoperability between Apps.

• Resource
• NIF
• 6 years ago - submitted by Maryann Martone

Registration toolbox written in pyTorch. Supports various image registration methods. Focuses on nonparametric registration approaches including stationary velocity fields and large discplacement diffeomorphic metric mapping models though simple affine registration is also possible. Allows for rapid prototyping of new image registration approaches and similarity measures.

• Resource
• NIF
• 6 years ago - submitted by Maryann Martone

Software R package for fast preranked gene set enrichment analysis. Allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.

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• RRID-Legacy
• 6 years ago - by Anonymous

Portal enables browsing, searching, and analysis of human genetic information linked to common metabolic diseases and traits, while protecting integrity and confidentiality of underlying data. Aggregates and analyzes genetic association results, epigenomic annotations, and results of computational prediction methods to provide data, visualizations, and tools in open access portal.

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• dkNET
• 6 years ago - submitted by Ko-Wei Lin

Portal for providing data and tools to promote understanding and treatment of type 1 diabetes and its complications.Enables browsing, searching, and analysis of human genetic information linked to type 1 diabetes and related traits, while protecting integrity and confidentiality of underlying data.Represents effort to coordinate collection and deposition of genomic and epigenomic data related to type 1 diabetes and its complications.

• Resource
• dkNET
• 6 years ago - submitted by Ko-Wei Lin

Software tool as plugin powered hybrid computing platform for deploying deep learning applications such as advanced image analysis tools. Runs on mobile and desktop environment cross different operating systems, can run in the browser, localhost, remote and cloud servers.

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• RRID-Legacy
• 6 years ago - submitted by Wei OUYANG

Software tool to calculate number of mapped exonic non duplicate reads in bam file containing RNA-Seq data.

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• SciCrunch
• 6 years ago - by Anonymous

Web tool for systematic reference data collection in land cover and use applications.Open source software tool for land monitoring. Systematic reference data collection tool for land cover and land use applications. Satellite image viewing and interpretation system developed by SERVIR joint efforts between NASA, FAO, US Forest Service and Google.

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• RRID-Legacy
• 6 years ago - by Anonymous

Software toolkit for rapid development of cloud native intelligent data pipelines for scientific data streams. Hierarchical approach to acquisition, analysis, and interpretation of image data. Developed in the project Hierarchical Analysis of Spatial and Temporal Data.

• Resource
• SciCrunch
• 6 years ago - submitted by Andreas Hellander