User: Sreeraj Thamban
Sreeraj Thamban • 90
- Reputation:
- 90
- Status:
- Trusted
- Location:
- Indian Institute of Science Education and Research
- Last seen:
- 2 months, 2 weeks ago
- Joined:
- 1 year, 1 month ago
- Email:
- s***************@iisertvm.ac.in
Posts by Sreeraj Thamban
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... Hello Biostars, Is it possible to plot all genes belonging to one particular pattern in EBSeq-HMM results as a line graph? ...
written 7 months ago by
Sreeraj Thamban • 90
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... Hello Biostars,
Is it possible to import Kallisto output to BaySeq? Which is the best way to do it?
Thanks in advance ...
written 7 months ago by
Sreeraj Thamban • 90
• updated
7 months ago by
Kevin Blighe ♦ 21k
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... Hi everyone recently I came across this [paper][1] where they used Bayesian Estimation of Temporal Regulation to analyze their time course RNASeq data. Can anyone suggest a good package in R or other software to do the same?
[1]: https://www.ncbi.nlm.nih.gov/pubmed/28904073 ...
written 7 months ago by
Sreeraj Thamban • 90
• updated
7 months ago by
andrew.j.skelton73 ♦ 5.0k
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... Hi Vijay, Did you try using Biomart? it has some useful function to fetch gene symbols. ...
written 7 months ago by
Sreeraj Thamban • 90
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Comment:
C: Time course experiment in RNASeq
... Hello Ron, I checked the EBseq package, but I am bit confused about interpretation the 'pattern' which is given by EBseq. It gives a list of patterns but what exactly those pattern means? ...
written 7 months ago by
Sreeraj Thamban • 90
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... Hello Biostars,
I have a time course experiment RNASeq data,one strain of bacteria and three time points 0h,1h,and3h. Which is the best method to identify the expression pattern of genes over time using this data? I want to generate a image like [this][1]
[1]: https://ibb.co/fKqasb ...
written 7 months ago by
Sreeraj Thamban • 90
• updated
7 months ago by
EagleEye • 5.3k
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... Hi Coster, I have a group of genes which are involved in a common pathway. I wanted to plot the overall trend of their expression pattern between treated and untreated samples. ...
written 7 months ago by
Sreeraj Thamban • 90
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8 follow
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... Helloo biostars,
I want visualise/plot the expression pattern of a set genes from my RNASeq data. Which are the best R packages or other softawares to do so? I came accross maSigPro and impulseDE but was not impressed by them.
Thanks in advance ...
written 7 months ago by
Sreeraj Thamban • 90
• updated
7 months ago by
Hussain Ather • 860
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... If you have basic knowledge in R you can use [ggplot2][1] to make good publication quality plots.
Here is an excellent [guide][2] for ggplot2.
HTH
[1]: http://ggplot2.org/
[2]: https://www.amazon.com/Graphics-Cookbook-Practical-Recipes-Visualizing/dp/1449316956 ...
written 7 months ago by
Sreeraj Thamban • 90
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... Hello Coster, Only the sequencing performed differently,library prep was same for both. ...
written 7 months ago by
Sreeraj Thamban • 90
Latest awards to Sreeraj Thamban
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Gene Set Enrichment Analysis after DESeq2
Scholar
7 months ago,
created an answer that has been accepted.
For A: How I can produce graphs like this
Supporter
7 months ago,
voted at least 25 times.
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