Curator Dashboard

Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data.

• Resource
• SciCrunch
• 7 years ago - submitted by Wenxi Wang

Software command line tool for performing direct coupling analysis of aligned categorical datasets. Used for analysis at scale of pan genomes of many bacteria. Incorporates correction for population structure, which adjusts for phylogenetic signal in data without requiring explicit phylogenetic tree.

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• RRID-Legacy
• 7 years ago - submitted by Chao Yang

Software tool for global direct coupling analysis of input genome alignments. Implements variant of pseudolikelihood maximization direct coupling analysis, with emphasis on optimizations that enable its use on genome scale. May be used to discover co evolving pairs of loci.Used for genome wide epistasis analysis.

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• RRID-Legacy
• 7 years ago - submitted by Chao Yang

Web tool for display, annotation and management of phylogenetic trees. Accessible with any modern web browser.

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• RRID-Legacy
• 7 years ago - submitted by Chao Yang

Software package to build, manipulate and display phylogenetic trees. Designed for building gene trees with known species tree and is highly efficient and accurate.

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• RRID-Legacy
• 7 years ago - submitted by Chao Yang

Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes.

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• RRID-Legacy
• 7 years ago - submitted by Chao Yang

Software package as system for rapidly aligning entire genomes. Alignment tool for DNA and protein sequences. Can align incomplete genomes.

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• RRID-Legacy
• 7 years ago - submitted by Chao Yang

Software tool as algorithm for identifying population structure using dense sequencing data. Can perform model based Bayesian clustering on large datasets, including full resequencing data.

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• RRID-Legacy
• 7 years ago - submitted by Chao Yang

Confocal microscope by Leica Microsystems to capture up to five true color channels simultaneously at high speed without need for trade-offs in multicolor experiments. Provides super resolution live cell imaging, simultaneous multicolor imaging, live specimen imaging thanks to fast acquisition rates, sample protection thanks to low phototoxicity.

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• RRID-Legacy
• 7 years ago - submitted by Anita Bandrowski

Software package for estimating and analyzing RNA velocities in single cells using dynamical modeling. RNA Velocity using dynamical modeling.

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• RRID-Legacy
• 7 years ago - submitted by Anita Bandrowski

Software package for analysis of expression dynamics in single cell RNA seq data. Enables estimations of RNA velocities of single cells by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols. Estimates RNA velocity in single cell RNA sequencing datasets. RNA velocity estimation in Python or R.

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• RRID-Legacy
• 7 years ago - submitted by Anita Bandrowski

Software plugin for bone image analysis in ImageJ. Used for standard bone measurements. Provides free, open source tools for trabecular geometry and whole bone shape analysis.

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• RRID-Legacy
• 7 years ago - by Anonymous

Collection of genes encoding proteins with strong support of mitochondrial localization. Inventory of genes encoding mitochondrial-localized proteins and their expression across 14 mouse tissues. Database is based on human and mouse RefSeq proteins that are mapped to NCBI Gene loci. MitoCarta 2.0 inventory provides molecular framework for system-level analysis of mammalian mitochondria.

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• RRID-Legacy
• 7 years ago - by Anonymous

Portal enabling web based visualization and analysis of multi omic data describing cell types in developing and adult brain, powered by gEAR and EpiViz. Release 1 on April 2019 includes single cell and bulk tissue RNAseq, ATACseq, and ChIPseq from fetal human prefrontal cortex, as well as from stem cell models of neural induction. Portal will expand to include multiple regions of developing and adult brain and additional analytical tools.

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• dkNET
• 7 years ago - submitted by Maryann Martone

Software used to analyze images obtained from microscope. ZEN Black is software Zeiss uses to run their laser-based instruments.

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• RRID-Legacy
• 7 years ago - by Anonymous

Web based analytics environment for genomic data arising from BRAIN Initiative Cell Census Network, based on AnnoJ browser. AnnoJ browser displays epigenomic data, including base resolution DNA methylation, RNA-Seq, ChIP-Seq, as well as annotations.

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• dkNET
• 7 years ago - submitted by Maryann Martone

Web tool as multiple sequence and structure alignment server. Automatically identifies homologs with known 3D structures for input sequences, derives structural constraints through structure based alignments and combines them with sequence constraints to construct consistency based multiple sequence alignments. Aligns sequences of multiple input structures, with output representing multiple structure based alignment refined in combination with sequence constraints.

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• RRID-Legacy
• 7 years ago - by Anonymous

Web tool to convert genome coordinates and genome annotation files between assemblies. Used to translate genomic coordinates from one assembly version into another and retrieves putative orthologous regions in other species using UCSC chained and netted alignments.

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• SciCrunch
• 7 years ago - by Anonymous

Web tool to show micro homology sequences striding over double strand break point created by CRISPR/Cas9 system. Used to search for CRISPR target site with micro-homology sequences. Used to predict deletion pattern.

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• RRID-Legacy
• 7 years ago - by Anonymous

Python implementation of conditional expectation maximization algorithm that estimates epigenetic landscapes and state of individuals and may be used to study nonlinear epigenetic aging. Fast conditional expectation maximization algorithm used to model epigenetic states associated with phenotype of interest. Can model non linear epigenetic trait associations directly without transformation of phenotype of interest.

• Resource
• SciCrunch
• 7 years ago - submitted by Colin Farrell