CufflinksCole Trapnell
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Evo DesignerArc Institute
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Related Products
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About
Cufflinks assemble transcripts, estimate their abundances and test for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols. Cufflinks was originally developed as part of a collaborative effort between the Laboratory for Mathematical and Computational Biology. In order to make it easy to install Cufflinks, we provide a few binary packages to save users from the occasionally frustrating process of building Cufflinks, which requires that you install the libraries. Cufflinks includes a number of tools for analyzing RNA-Seq experiments. Some of these tools can be run on their own, while others are pieces of a larger workflow.
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About
Evo Designer is an advanced tool developed by the Arc Institute, leveraging the capabilities of the Evo 2 genomic foundation model to facilitate DNA sequence generation and analysis. This platform enables users to input nucleotide sequences or specify organisms, prompting the model to generate corresponding DNA sequences. It provides comprehensive annotations of coding regions and, for prokaryotic sequences, offers 3D protein visualizations utilizing ESMFold. Additionally, Evo Designer evaluates sequences by scoring their perplexity and per-nucleotide entropy, assisting researchers in assessing sequence complexity and variability. The underlying Evo 2 model is trained on over 9 trillion nucleotides from a diverse array of prokaryotic and eukaryotic genomes, employing a deep learning architecture that models biological sequences at single-nucleotide resolution with a context window extending up to 1 million tokens.
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Platforms Supported
Windows
Mac
Linux
Cloud
On-Premises
iPhone
iPad
Android
Chromebook
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Platforms Supported
Windows
Mac
Linux
Cloud
On-Premises
iPhone
iPad
Android
Chromebook
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Audience
Scientists requiring a solution to analyze their RNA-Seq samples
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Audience
Genetic engineers requiring an AI-driven platform to generate and analyze DNA sequences, facilitating advancements in genomic research and synthetic biology
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Support
Phone Support
24/7 Live Support
Online
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Support
Phone Support
24/7 Live Support
Online
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API
Offers API
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API
Offers API
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Screenshots and Videos |
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Pricing
Free
Free Version
Free Trial
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Pricing
No information available.
Free Version
Free Trial
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Reviews/
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Reviews/
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Training
Documentation
Webinars
Live Online
In Person
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Training
Documentation
Webinars
Live Online
In Person
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Company InformationCole Trapnell
Founded: 2017
United States
cole-trapnell-lab.github.io/cufflinks/
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Company InformationArc Institute
United States
arcinstitute.org/tools/evo/evo-designer
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Categories |
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Integrations
Evo 2
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