User: Sreeraj Thamban

gravatar for Sreeraj Thamban
Reputation:
100
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Location:
Indian Institute of Science Education and Research
Last seen:
5 months, 2 weeks ago
Joined:
1 year, 4 months ago
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s***************@iisertvm.ac.in

Posts by Sreeraj Thamban

<prev • 43 results • page 1 of 5 • next >
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Plotting Results in EBSeq-HMM
... Hello Biostars, Is it possible to plot all genes belonging to one particular pattern in EBSeq-HMM results as a line graph? ...
ebseq-hmm rna-seq written 10 months ago by Sreeraj Thamban100
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Kallisto counts to Bayseq
... Hello Biostars, Is it possible to import Kallisto output to BaySeq? Which is the best way to do it? Thanks in advance ...
rna-seq written 10 months ago by Sreeraj Thamban100 • updated 10 months ago by Kevin Blighe28k
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Bayesian Estimation of Temporal Regulation-RNASeq
... 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 ...
rna-seq written 10 months ago by Sreeraj Thamban100 • updated 10 months ago by andrew.j.skelton735.3k
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Comment: C: Fetching NCBI gene symbols from NCBI protein ids or GI identifiers
... Hi Vijay, Did you try using Biomart? it has some useful function to fetch gene symbols. ...
written 10 months ago by Sreeraj Thamban100
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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 10 months ago by Sreeraj Thamban100
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Time course experiment in RNASeq
... 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 ...
rna-seq written 10 months ago by Sreeraj Thamban100 • updated 10 months ago by EagleEye5.6k
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Comment: C: Best tools for Visualing RNASeq data
... 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 10 months ago by Sreeraj Thamban100
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Best tools for Visualing RNASeq data
... 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 ...
deseq2 rna-seq written 10 months ago by Sreeraj Thamban100 • updated 10 months ago by Hussain Ather880
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Answer: A: How I can produce graphs like this
... 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 10 months ago by Sreeraj Thamban100
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Comment: C: Paired end vs Single end Differential gene expression analysis
... Hello Coster, Only the sequencing performed differently,library prep was same for both. ...
written 11 months ago by Sreeraj Thamban100

Latest awards to Sreeraj Thamban

Popular Question 9 months ago, created a question with more than 1,000 views. For Gene Set Enrichment Analysis after DESeq2
Scholar 10 months ago, created an answer that has been accepted. For A: How I can produce graphs like this
Supporter 11 months ago, voted at least 25 times.

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