Cufflinks

Cufflinks

Cole Trapnell
PacBio

PacBio

Pacific Biosciences (PacBio)
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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.

About

PacBio (Pacific Biosciences) is a premier life science technology company that is designing, developing and manufacturing advanced sequencing solutions to help scientists and clinical researchers resolve genetically complex problems. Our products and technologies stem from two highly differentiated core technologies focused on accuracy, quality and completeness which include our HiFi long-read sequencing and our SBB® short-read sequencing technologies. Our products address solutions across a broad set of research applications including human germline sequencing, plant and animal sciences, infectious disease and microbiology, oncology, and other emerging applications. The Revio system adds affordability, high throughput, and ease of use to a foundation of long reads, exceptional accuracy, and direct methylation detection. The Onso system is an innovative benchtop short-read DNA sequencing platform with an extraordinary level of accuracy using PacBio sequencing by binding.

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

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

Audience

Scientists requiring a solution to analyze their RNA-Seq samples

Audience

Scientists in the field of genomics looking for highly-accurate genomic analysis systems

Support

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

Support

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

API

Offers API Not Supported

API

Offers API Supported

Screenshots and Videos

Screenshots and Videos

Pricing

Free
Free Version Supported
Free Trial Not Supported

Pricing

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

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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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

Training

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

Training

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

Company Information

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

Company Information

Pacific Biosciences (PacBio)
Founded: 2004
United States
www.pacb.com/products-and-services/

Alternatives

QIAGEN CLC Genomics Workbench

QIAGEN CLC Genomics Workbench

QIAGEN Digital Insights

Alternatives

Categories

Categories

LIMS Supported

Integrations

No info available.

Integrations

No info available.
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