Request to install our developed pipeline LncRAnalyzer to Galaxy server from Galaxy toolshed
Dear Sir/Madam, I hope this message finds you well. We are pleased to inform you that we have developed an automated analysis pipeline named LncRAnalyzer [ https://gitlab.com/nikhilshinde0909/LncRAnalyzer] for the identification of long non-coding RNAs (lncRNAs) and non-protein-coding transcripts (NPCTs) from RNA-Seq data. The workflow is comprehensive and integrates eight established bioinformatics tools, including a dedicated module for lncRNA conservation analysis. Currently, LncRAnalyzer supports execution in Conda, Docker, and Singularity environments, making it flexible and accessible across various systems. However, in order to further enhance its usability and reach a broader research community, we are keen on making it available via the Galaxy platform, which is widely used for RNA-Seq data analysis due to its user-friendly interface and reproducible workflow environment. In this regard, we uploaded our pipeline at Galaxy-toolshed [ https://toolshed.g2.bx.psu.edu/view/nikhilshinde0909/lncranalyzer/9dd1c1cb28...] and Galaxy-testtolshed [ https://testtoolshed.g2.bx.psu.edu/view/nikhilshinde0909/lncranalyzer/db9194...] but to install it at Galaxy-plantform [https://usegalaxy.org/] admin need to be do it. Therefore, we kindly request you to install this workflow into Galaxy from Galaxy-toolshed or Galaxy-testtoolshed. We believe that this workflow will be highly valuable to the Indian bioinformatics community working on transcriptome analysis, particularly in the domain of non-coding RNAs. Thank you very much for your time and consideration. We look forward to your positive response. Warm regards, Shinde Nikhil SRM Institute of Science and Technology, SRM nagar, Kattankulanthur, Chengalpattu district, Tamil Nadu 603203 India
Excellent! Heartiest congratulations, sure,Nikhil Regards Prash Prashanth N Suravajhala, Ph.D. Professor(Research), Systems Genomics Lab, Department of Biosciences, Room # 323D, AB-3, Manipal University Jaipur, Dehmi Kalan 303007, India. Founder, Bioclues.org Group page: http://www.bioinformatics.org/wiki/Prash Twitter: @prashbio "One rule is important in science- only courageous people win " ~ Max Planck On Sat, 24 May, 2025, 15:23 SHINDE NIKHIL DHANAJI (RC2113010011030), < sd1172@srmist.edu.in> wrote:
Dear Sir/Madam,
I hope this message finds you well.
We are pleased to inform you that we have developed an automated analysis pipeline named LncRAnalyzer [ https://gitlab.com/nikhilshinde0909/LncRAnalyzer] for the identification of long non-coding RNAs (lncRNAs) and non-protein-coding transcripts (NPCTs) from RNA-Seq data. The workflow is comprehensive and integrates eight established bioinformatics tools, including a dedicated module for lncRNA conservation analysis.
Currently, LncRAnalyzer supports execution in Conda, Docker, and Singularity environments, making it flexible and accessible across various systems. However, in order to further enhance its usability and reach a broader research community, we are keen on making it available via the Galaxy platform, which is widely used for RNA-Seq data analysis due to its user-friendly interface and reproducible workflow environment.
In this regard, we uploaded our pipeline at Galaxy-toolshed [ https://toolshed.g2.bx.psu.edu/view/nikhilshinde0909/lncranalyzer/9dd1c1cb28...] and Galaxy-testtolshed [ https://testtoolshed.g2.bx.psu.edu/view/nikhilshinde0909/lncranalyzer/db9194...] but to install it at Galaxy-plantform [https://usegalaxy.org/] admin need to be do it. Therefore, we kindly request you to install this workflow into Galaxy from Galaxy-toolshed or Galaxy-testtoolshed.
We believe that this workflow will be highly valuable to the Indian bioinformatics community working on transcriptome analysis, particularly in the domain of non-coding RNAs.
Thank you very much for your time and consideration. We look forward to your positive response.
Warm regards,
Shinde Nikhil SRM Institute of Science and Technology, SRM nagar, Kattankulanthur, Chengalpattu district, Tamil Nadu 603203 India _______________________________________________ India mailing list -- india@lists.galaxyproject.org To unsubscribe send an email to india-leave@lists.galaxyproject.org
(could be repeat for some of you, as earlier my email did not went through, sending the email again) Wonderful Nikhil. Very glad to know that SRM University is taking nice steps to use the potential of the Galaxy framework. From your college Anguraj attended Galaxy Bharat meetings <https://www.galaxyproject.in/>. Hope to see you more attending the meetings. It would be great if you can add your repository into the Galaxy Bharat umbrella. If you are willing to do that, please do attend the meetings and give a stage for your tool exposure to others who can use it further. Regards, *________________* Dr. Kiran K Telukunta <https://www.linkedin.com/in/kiran-k-telukunta-5455525/> TMS Foundation <https://bharatyuva.org/> | IT & Bioinformatics w: bharatyuva.org e: kiran.telukunta@indiayouth.info Social links: [image: created with MySignature.io] <https://www.linkedin.com/in/kiran-k-telukunta-5455525/> [image: created with MySignature.io] <https://www.researchgate.net/profile/Kiran_Kumar_Telukunta> [image: created with MySignature.io] <https://gitlab.com/telukir> [image: created with MySignature.io] <https://github.com/telukir> [image: created with MySignature.io] <https://twitter.com/telukir> On Sat, 24 May 2025 at 11:53, SHINDE NIKHIL DHANAJI (RC2113010011030) < sd1172@srmist.edu.in> wrote:
Dear Sir/Madam,
I hope this message finds you well.
We are pleased to inform you that we have developed an automated analysis pipeline named LncRAnalyzer [ https://gitlab.com/nikhilshinde0909/LncRAnalyzer] for the identification of long non-coding RNAs (lncRNAs) and non-protein-coding transcripts (NPCTs) from RNA-Seq data. The workflow is comprehensive and integrates eight established bioinformatics tools, including a dedicated module for lncRNA conservation analysis.
Currently, LncRAnalyzer supports execution in Conda, Docker, and Singularity environments, making it flexible and accessible across various systems. However, in order to further enhance its usability and reach a broader research community, we are keen on making it available via the Galaxy platform, which is widely used for RNA-Seq data analysis due to its user-friendly interface and reproducible workflow environment.
In this regard, we uploaded our pipeline at Galaxy-toolshed [ https://toolshed.g2.bx.psu.edu/view/nikhilshinde0909/lncranalyzer/9dd1c1cb28...] and Galaxy-testtolshed [ https://testtoolshed.g2.bx.psu.edu/view/nikhilshinde0909/lncranalyzer/db9194...] but to install it at Galaxy-plantform [https://usegalaxy.org/] admin need to be do it. Therefore, we kindly request you to install this workflow into Galaxy from Galaxy-toolshed or Galaxy-testtoolshed.
We believe that this workflow will be highly valuable to the Indian bioinformatics community working on transcriptome analysis, particularly in the domain of non-coding RNAs.
Thank you very much for your time and consideration. We look forward to your positive response.
Warm regards,
Shinde Nikhil SRM Institute of Science and Technology, SRM nagar, Kattankulanthur, Chengalpattu district, Tamil Nadu 603203 India _______________________________________________ India mailing list -- india@lists.galaxyproject.org To unsubscribe send an email to india-leave@lists.galaxyproject.org
participants (3)
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Kiran K Telukunta -
Prash -
SHINDE NIKHIL DHANAJI (RC2113010011030)