Curator Dashboard

Software application that provides sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, agarose gel simulation and a variety of other functions.

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• RRID-Legacy
• 9 years ago - by Anonymous

Interactive analysis notebook environment that streamlines genomics research by interleaving text, multimedia, and executable code into unified, sharable, reproducible “research narratives.” It integrates the dynamic capabilities of notebook systems with an investigator-focused, simple interface that provides access to hundreds of genomic tools without the need to write code.

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• SciCrunch
• 9 years ago - submitted by James Go

Kit for assessing motor function and endurance in mice and rats. IITC’s Rotarod Test is capable of having up to five mice or rats tested at a time standard.

• RRID-Legacy
• 9 years ago - submitted by Neil Ford

A script to convert Bam alignments into a wig representation file.

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• RRID-Legacy
• 9 years ago - by Anonymous

Tools for querying and analysis of genomic data. These libraries provide a useful interface for working with bioinformatic data. Many bioinformatic data analysis revolves around working with tables of information, including lists of genomic annotation (genes, promoters, etc.) or defined regions of interest (epigenetic enrichment, transcription factor binding sites, etc.). This library works with these tables and provides a set of common tools for working with them. Opening and saving common tab-delimited text formats Support for BED, GFF, VCF, narrowPeak files Scoring intervals with datasets from microarray and sequencing ChIPSeq, RNASeq, microarray expression Support for Bam, BigWig, BigBed, wig, and USeq data formats Intersection with other known annotation Works with any genomic annotation in GTF, GFF3, and UCSC formats The libraries provide a unified and integrated approach to analyses. In many cases, they provide an abstraction layer over a variety of different specialized BioPerl and related modules. Instead of writing numerous scripts specialized for each data format (wig, bigWig, Bam), one script can now work with any data format.

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• RRID-Legacy
• 9 years ago - by Anonymous

A commercial software package that works with Carl Zeiss microscopy; AIM 4.2 software.

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• RRID-Legacy
• 9 years ago - by Anonymous

A variant vcf file analysis tool.

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• RRID-Legacy
• 9 years ago - by Anonymous

The Black Dog Institute is dedicated to understanding, preventing and treating mental illness. We are about creating a world where mental illness is treated with the same level of concern, immediacy and seriousness as physical illness; where scientists work to discover the causes of illness and new treatments, and where discoveries are immediately put into practice through health services, technology and community education.

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• RRID-Legacy
• 9 years ago - by Anonymous

Disease portal for Hepatitis that provides information about causes, symptoms, treatments, and other characteristics of Hepatitis. This webpage is curated by Verywell, a health and wellness organization.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

software for ChemiDoc Touch Imaging System,Bio-Rad

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• SciCrunch
• 9 years ago - by Anonymous

Oncotopix Discovery is a comprehensive solution powered for whole slide image analysis of tissue sections, TMA slides across any image analysis application. Simple to program also for scientists without an IT background.

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• RRID-Legacy
• 9 years ago - by Anonymous

Implements an algorithm to conduct advanced gene set enrichment analysis on the results of genomics experiments. Simillion C, Liechti R, Lischer HE, Ioannidis V, Bruggmann R. Avoiding the pitfalls of gene set enrichment analysis with SetRank. BMC bioinformatics. 2017;18(1):151. doi: 10.1186/s12859-017-1571-6.

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• RRID-Legacy
• 9 years ago - by Anonymous

The main purpose of Cufflinks.cuffmerge is to merge together several Cufflinks assemblies, making it easier to produce an assembly GTF file suitable for use with Cufflinks.cuffdiff. Cufflinks.cuffmerge also runs Cuffcompare in the background and automatically filters out transcribed fragments (transfrags) that are likely to be artifacts. Trapnell C, Hendrickson D,Sauvageau S, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature Biotechnology. 2013;31:46-53.

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• RRID-Legacy
• 9 years ago - by Anonymous

Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates.

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• RRID-Legacy
• 9 years ago - by Anonymous

Sequence analysis software for rt-qPCR analysis. It establishes standard curves, calculates delta delta Ct and automatically determines the ideal threshold setting for each run.

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• RRID-Legacy
• 9 years ago - submitted by Keiji Honda

Software toolkit for analyzing and visualizing data of single cell qPCR/RNA-seq. It offers methods for identifying gene expression and mutation patterns at the single-cell level and is designed for use with Biomark and C1 systems.

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• RRID-Legacy
• 9 years ago - submitted by Keiji Honda

A web interface for the scoring of biomedical digital objects by user evaluation according to the FAIR data principles: Findability, Accessibility, Interoperability, and Reusability. Prototype currently available at: http://amp.pharm.mssm.edu/fairshake

• SciCrunch
• 9 years ago - submitted by Anita Bandrowski

ARCHS4 provides access to gene counts from HiSeq 2000 and HiSeq 2500 platforms for human and mouse experiments from GEO and SRA. The website enables downloading of the data in H5 format for programmatic access as well as a 3-dimensional view of the sample and gene spaces. Search features allow browsing of the data by meta data annotation, ability to submit your own up and down gene sets, and explore matching samples enriched for annotated gene sets. Selected sample sets can be downloaded into a tab separated text file through auto-generated R scripts for further analysis. Reads are aligned with Kallisto using a custom cloud computing platform. Human samples are aligned against the GRCh38 human reference genome, and mouse samples against the GRCm38 mouse reference genome.

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• SciCrunch
• 9 years ago - submitted by Anita Bandrowski

Software tool for aggregation and analysis of gene expression signatures from related studies.Used to aggregate and analyze gene expression signatures extracted from GEO by crowd using GEO2Enrichr. Used to view aggregated report that provides global, interactive views, including enrichment analyses, for collections of signatures from multiple studies sharing biological theme.

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• SciCrunch
• 9 years ago - submitted by Anita Bandrowski

Clustergrammer is a web-based tool for visualizing and analyzing high-dimensional data as interactive and shareable hierarchically clustered heatmaps. Clustergrammer enables intuitive exploration of high-dimensional data and has several optional biology-specific features.

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• SciCrunch
• 9 years ago - submitted by Anita Bandrowski