Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Omics Playground Platform

    Dear Seqanswers' community,

    We would like to introduce a new platform for the analysis and visualisation of transcriptomics and proteomics data that we recently published in NAR Genomics and Bioinformatics (here).

    The platform is designed for ease of use once installed and requires users to input four flat text files (including a raw read counts file) as input. Examples of the format are provided in the documentation.

    The platform can be installed locally on various operating systems (including Windows) via a docker file, while the open source code is available on github:

    Docker: https://hub.docker.com/r/bigomics/omicsplayground

    Github: https://github.com/bigomics/omicsplayground

    It can perform a wide range of analyses, including statistical comparison with Connectivity Map expression profiles. It can also intersect different algorithms to provide more stringent and reliable hits (for example, at the gene expression level it can intersect the results of up to 8 different methodologies used in EdgeR, Deseq2 and limma) . A more exhaustive list of functions is described in the documentation.

    We also have a google group where you can contact us with questions:

    Google Group: https://groups.google.com/forum/#!forum/omicsplayground

    We would appreciate your feedback on the platform.

    We are planning to develop an open access web-based version in the near future as well, to make the platform more accessible.
    Last edited by AxelM; 12-10-2019, 03:26 AM.

Latest Articles

Collapse

  • seqadmin
    Strategies for Sequencing Challenging Samples
    by seqadmin


    Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
    03-22-2024, 06:39 AM
  • seqadmin
    Techniques and Challenges in Conservation Genomics
    by seqadmin



    The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

    Avian Conservation
    Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
    03-08-2024, 10:41 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 03-27-2024, 06:37 PM
0 responses
13 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-27-2024, 06:07 PM
0 responses
11 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-22-2024, 10:03 AM
0 responses
53 views
0 likes
Last Post seqadmin  
Started by seqadmin, 03-21-2024, 07:32 AM
0 responses
69 views
0 likes
Last Post seqadmin  
Working...
X