Curator Dashboard

Animal Cage Enclosures for use in in vivo models that require control of experimental gases such as O2, CO2, NO, or CO. May be used together with gas controllers from BioSpherix. Chamber is outfitted with adjustable ventilation holes which permit ventilation of animal vapors and gases while simultaneously ensuring stable control of experimental conditions within. Available in three standard sizes.

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• SciCrunch
• 5 years ago - submitted by Ray Gould

Controller for live cell microscopy provides two identical streams of any mix of oxygen and carbon dioxide gas without use of premixed gas cylinders. Eliminates need for pre-mixed gas. Controller is used primarily to pre-condition perfusion media while simultaneously conditioning headspace above culture.

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• SciCrunch
• 5 years ago - submitted by Ray Gould

Hypoxia cell culture system includes hypoxia incubator and cell culture hood with glove sleeves.

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• SciCrunch
• 5 years ago - submitted by Ray Gould

Software tool to combine multiple subreads of same SMRTbell molecule using statistical model to produce one highly accurate consensus sequence, also called HiFi read, along with base quality values. This tool powers Circular Consensus Sequencing workflow in SMRT Link.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software tool to purge haplotigs and overlaps in assembly based on read depth.Used for haplotypic duplication identification. Designed to remove haplotigs and contig overlaps in a de novo assembly based on read depth.

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• RRID-Legacy
• 5 years ago - by Anonymous

Visualization and analysis software for Hi-C data.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software tool for computing scaffold ordering that maximizes colinearity to collection of maps, including genetic, physical or comparative maps into final chromosome build.Robust scaffold ordering based on multiple maps.

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• RRID-Legacy
• 5 years ago - by Anonymous

a package for automated de novo identification of repeat families from genomic sequences Proper identification of repetitive sequences is an essential step in genome analysis. The RECON package performs de novo identification and classification of repeat sequence families from genomic sequences. The underlying algorithm is based on extensions to the usual approach of single linkage clustering of local pairwise alignments between genomic sequences. Specifically, our extensions use multiple alignment information to define the boundaries of individual copies of the repeats and to distinguish homologous but distinct repeat element families. RECON should be useful for first-pass automatic classification of repeats in newly sequenced genomes.

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• RRID-Legacy
• 5 years ago - by Anonymous

Database of repetitive DNA elements.Database of prototypic sequences representing repetitive DNA from different eukaryotic species. Used in genome sequencing projects worldwide as reference collection for masking and annotation of repetitive DNA.

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• RRID-Legacy
• 5 years ago - by Anonymous

Open collection of Transposable Element DNA sequence alignments, hidden Markov Models, consensus sequences, and genome annotations.Dfam 3.2 provides early access to uncurated, de novo generated families.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software pipeline for predicting and scoring hints (in form of introns, start and stop codons) in genome of interest by mapping and spliced aligning predicted genes to database of reference protein sequences.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software tool for assembly free construction of UTRs from short read RNA-Seq data on basis of coding sequence annotation.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed eggNOG v5.0 clusters and phylogenies.

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• RRID-Legacy
• 5 years ago - by Anonymous

Curated component of UniProtKB (produced by the UniProt consortium). It contains hundreds of thousands of protein descriptions, including function, domain structure, subcellular location, post-translational modifications and functionally characterized variants.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software tool for phylogenomic inference.

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• RRID-Legacy
• 5 years ago - by Anonymous

Public knowledge base for information on evolutionary timescale of life. Data from thousands of published studies are assembled into searchable tree of life scaled to time.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software package for estimating absolute rates of molecular evolution and divergence times on phylogenetic tree. Divergence time estimation on phylogenies.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software tool as set of analysis pipelines that process Chromium Single Cell ATAC data. Cell Ranger ATAC includes four pipelines relevant to single cell chromatin accessibility experiments.Used to investigate number of chromatin-accessibility signatures.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software python-based command line interface for processing .bam files with mitochondrial reads and generating high-quality heteroplasmy estimation from sequencing data. This package places a special emphasis on mitochondrial genotypes generated from single-cell genomics data, primarily mtscATAC-seq, but is generally applicable across other assays.

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• RRID-Legacy
• 5 years ago - by Anonymous

Software framework for analysis of single cell chromatin data. Used for analysis, interpretation, and exploration of single cell chromatin datasets including datasets that co-assay DNA accessibility with gene expression, protein abundance, and mitochondrial genotype. Analysis of single-cell chromatin data including peak calling, quantification, quality control, dimension reduction, clustering, integration with single-cell gene expression datasets, DNA motif analysis, and interactive visualization.

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• RRID-Legacy
• 5 years ago - by Anonymous