User: k.nirmalraman

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k.nirmalraman1.1k
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Germany
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1 month ago
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8 years, 3 months ago
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k************@gmail.com

I am a molecular biologist who have started working on NGS techniques for transcriptomics, genomics and epigenetics.

Posts by k.nirmalraman

<prev • 134 results • page 1 of 14 • next >
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Answer: A: Heatmaps by pheatmap
... Another interesting heatmap package is ComplexHeatmap https://jokergoo.github.io/ComplexHeatmap-reference/book/ ...
written 5 weeks ago by k.nirmalraman1.1k
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Comment: C: Transcript Models In Circos
... Hi Sean, I am looking for something like it now... Did you get to what you tried with circos? ...
written 6.9 years ago by k.nirmalraman1.1k
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Circos: Plotting Various Transcripts Of A Gene?
... Hello, I was wondering would it be possible to plot various transcripts (isoforms) of a given gene in Circos. Any pointers would be really helpful. In particular, I am aware I could use the tile feature, but I am still wondering would it be possible to generate something like exon intron map on ...
written 6.9 years ago by k.nirmalraman1.1k • updated 6.8 years ago by Biostar ♦♦ 20
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Comment: C: Mouse Genome Build And Gtf Conflict In Tophat Downloads
... Thanks!! That sounds promising.. I should nevertheless try Ensembl Annotations!! ...
written 7.0 years ago by k.nirmalraman1.1k
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Mouse Genome Build And Gtf Conflict In Tophat Downloads
... Dear All, I have been using the sequences and annotations for mouse from tophat website here and specifically the UCSC version mm10. I see that the sequences (genome.fa) contains Chr1- Chr19, ChrX, ChrY and ChrM... while the corresponding GTF file contains features for these random chromosome se ...
chromosome written 7.0 years ago by k.nirmalraman1.1k • updated 7.0 years ago by Devon Ryan98k
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Comment: C: Fitting Distribution Of The Gene Expression Levels Of Rna Seq Data
... I thought this applies for the distribution of say Gene-i across samples. I understood it that way from the DE Seq Paper Equation 1: K i j ~ NB ( μ i j , σ i ...
written 7.0 years ago by k.nirmalraman1.1k
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Fitting Distribution Of The Gene Expression Levels Of Rna Seq Data
... I am trying to fit a distribution of the gene expression (DESeq Normalized counts) of each sample from a RNA Seq data. And I came across this paper where they describe that the expression levels of genes have a Bimodal distribution. . I was wondering would this be true for the count data as well o ...
written 7.0 years ago by k.nirmalraman1.1k
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Comment: C: Strategy For Rna Seq Normalization Across Different Tissue Samples With Differen
... Certainly, in an RNA-Seq experiment of case vs control, we would like to capture both Q1 and Q2. If we conveniently ignore Q1 (or Q2) how relevant and accurate is our final set of genes to our experimental objective? I can agree that we would have to perform two step normalization as you propose, b ...
written 7.1 years ago by k.nirmalraman1.1k
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Strategy For Rna Seq Normalization Across Different Tissue Samples With Different Cell Density.
... Hello All, This is another question about RNA Seq data normalization. Often, I have read papers using ERCC spike in as control for identifying experimental bias that may occur due to RNA species length and concentration. Then I came across this paper: Revisiting Global Gene Expression Analysis, wh ...
normalization rna-seq written 7.1 years ago by k.nirmalraman1.1k • updated 7.0 years ago by Charles Warden8.0k
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Comment: C: Is It Valid To Convert A Fold Change Matrix Into Z Score?
... Visualization is not the key point, though that is one of the objective. The key thing is we need to normalize the data to be able to compare them against each other. This is something I feel would be correct to do, before concluding something biologically. ...
written 7.2 years ago by k.nirmalraman1.1k

Latest awards to k.nirmalraman

Scholar 5 weeks ago, created an answer that has been accepted. For A: Heatmaps by pheatmap
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Phd Candidate Interview Questions For A Mixed Lab/Bioinformatics Project
Great Question 3.9 years ago, created a question with more than 5,000 views. For Tophat - Htseq Count? How Can I Improve The Mapping Percentage For Single End Reads
Great Question 3.9 years ago, created a question with more than 5,000 views. For Fasta Length
Great Question 3.9 years ago, created a question with more than 5,000 views. For How To Run The Meme Motif Discovery Software On A Large Dataset?
Great Question 3.9 years ago, created a question with more than 5,000 views. For How To Get Annotation For Bed File From Another Bed File
Great Question 3.9 years ago, created a question with more than 5,000 views. For Is There A Easy Way To Find The Gene Annotations For Features In Bed File?
Good Question 3.9 years ago, asked a question that was upvoted at least 5 times. For Scatter Plot For Correlations With Heatdensity
Great Question 3.9 years ago, created a question with more than 5,000 views. For Gsva Analysis In R: Unable To Identify Method For Function
Guru 3.9 years ago, received more than 100 upvotes.
Great Question 3.9 years ago, created a question with more than 5,000 views. For Scatter Plot For Correlations With Heatdensity
Great Question 3.9 years ago, created a question with more than 5,000 views. For How To Transform From Rna-Seq Deseq To Limma Voom() And Makecontrasts
Great Question 3.9 years ago, created a question with more than 5,000 views. For Deseq: Multiple Conditions Testing
Great Question 3.9 years ago, created a question with more than 5,000 views. For How To Determine Overlaps From Coordinates
Great Question 3.9 years ago, created a question with more than 5,000 views. For Mapping Of Bisulfite Sequencing Reads
Epic Question 3.9 years ago, created a question with more than 10,000 views. For Is There A Easy Way To Find The Gene Annotations For Features In Bed File?
Epic Question 3.9 years ago, created a question with more than 10,000 views. For Scatter Plot For Correlations With Heatdensity
Epic Question 3.9 years ago, created a question with more than 10,000 views. For How To Transform From Rna-Seq Deseq To Limma Voom() And Makecontrasts
Epic Question 3.9 years ago, created a question with more than 10,000 views. For Is It Possible To Fix The Scale In Ggplot?
Epic Question 3.9 years ago, created a question with more than 10,000 views. For Can We Compare Two Different Rna-Seq Experiments?
Popular Question 3.9 years ago, created a question with more than 1,000 views. For Cell Type Composition In A Tissue Based On Gene Marker Expression
Appreciated 3.9 years ago, created a post with more than 5 votes. For A: Sequence Logos With Weblogo Scale
Teacher 3.9 years ago, created an answer with at least 3 up-votes. For A: Phd Candidate Interview Questions For A Mixed Lab/Bioinformatics Project
Appreciated 3.9 years ago, created a post with more than 5 votes. For A: What More Than Gene Expression Analysis Can I Do With My Rna-Seq Data?

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