Cufflinks

Cufflinks

Cole Trapnell
Biohub Cufflinks

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Biohub:

About

Biohub is an open platform for building on the world model of protein biology. It provides access to the ESM family of models, including ESMC, ESMFold2, and ESM3, along with interactive tools and developer resources for protein science research. ESMC is a state-of-the-art protein language model trained on billions of evolutionary sequences, building representations that capture fundamental mechanisms of protein structure and function. It powers functional analysis, structure prediction, protein design, and the exploration of evolutionary relationships between proteins. ESMFold2 predicts high-resolution, all-atom 3D structures of biomolecular complexes directly from sequence, with optional multiple sequence alignment input for enhanced accuracy on challenging targets. ESM3 jointly models sequence, structure, and function, enabling controllable generation of novel proteins by conditioning on any combination of these modalities.
Cufflinks:

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.
Biohub:

Platforms Supported

Windows Not Supported
Mac Not Supported
Linux Not Supported
Cloud Supported
On-Premises Not Supported
iPhone Not Supported
iPad Not Supported
Android Not Supported
Chromebook Not Supported
Cufflinks:

Platforms Supported

Windows Supported
Mac Supported
Linux Supported
Cloud Not Supported
On-Premises Not Supported
iPhone Not Supported
iPad Not Supported
Android Not Supported
Chromebook Not Supported
Biohub:

Audience

Computational biologists and protein engineering teams that need AI models, structure prediction tools, and protein-scale datasets for discovery and design
Cufflinks:

Audience

Scientists requiring a solution to analyze their RNA-Seq samples
Biohub:

Support

Phone Support Not Supported
24/7 Live Support Not Supported
Online Supported
Cufflinks:

Support

Phone Support Not Supported
24/7 Live Support Not Supported
Online Supported
Biohub:

API

Offers API Supported
Cufflinks:

API

Offers API Not Supported
Biohub:

Screenshots and Videos

Cufflinks:

Screenshots and Videos

Biohub:

Pricing

No information available.
Free Version Not Supported
Free Trial Not Supported
Cufflinks:

Pricing

Free
Free Version Supported
Free Trial Not Supported
Biohub:

Reviews/Ratings

Overall 0.0 / 5
ease 0.0 / 5
features 0.0 / 5
design 0.0 / 5
support 0.0 / 5

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Cufflinks:

Reviews/Ratings

Overall 0.0 / 5
ease 0.0 / 5
features 0.0 / 5
design 0.0 / 5
support 0.0 / 5

This software hasn't been reviewed yet. Be the first to provide a review:

Review this Software
Biohub:

Training

Documentation Supported
Webinars Not Supported
Live Online Supported
In Person Not Supported
Cufflinks:

Training

Documentation Supported
Webinars Not Supported
Live Online Not Supported
In Person Not Supported
Biohub:

Company Information

Biohub
Founded: 2016
United States
biohub.ai/
Cufflinks:

Company Information

Cole Trapnell
Founded: 2017
United States
cole-trapnell-lab.github.io/cufflinks/
Biohub:

Alternatives

ESMC

ESMC

Biohub
Cufflinks:

Alternatives

QIAGEN CLC Genomics Workbench

QIAGEN CLC Genomics Workbench

QIAGEN Digital Insights
Biohub:
ESMFold2

ESMFold2

Biohub
Cufflinks:
Biohub:
HyperProtein

HyperProtein

Hypercube
Cufflinks:
Biohub:
Cufflinks:
Biohub:
Evo 2

Evo 2

Arc Institute
Cufflinks:
Biohub:

Categories

AI Science Supported
Bioinformatics Supported
Cufflinks:

Categories

Biohub:

Integrations

ESMC Supported
ESMFold2 Supported
Cufflinks:

Integrations

ESMC Not Supported
ESMFold2 Not Supported
Biohub:
Claim Biohub and update features and information
Claim Biohub and update features and information
Cufflinks:
Claim Cufflinks and update features and information
Claim Cufflinks and update features and information