User: k.nirmalraman

gravatar for k.nirmalraman
k.nirmalraman900
Reputation:
900
Status:
Trusted
Location:
Germany
Last seen:
10 months, 2 weeks ago
Joined:
5 years, 3 months ago
Email:
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 • 133 results • page 1 of 14 • next >
0
votes
2
answers
2.4k
views
2
answers
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 3.9 years ago by k.nirmalraman900
2
votes
0
answers
1.5k
views
0
answers
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 3.9 years ago by k.nirmalraman900 • updated 3.8 years ago by Biostar ♦♦ 20
0
votes
1
answer
2.6k
views
1
answers
Comment: C: Mouse Genome Build And Gtf Conflict In Tophat Downloads
... Thanks!! That sounds promising.. I should nevertheless try Ensembl Annotations!! ...
written 4.0 years ago by k.nirmalraman900
4
votes
1
answer
2.6k
views
1
answer
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 4.0 years ago by k.nirmalraman900 • updated 4.0 years ago by Devon Ryan76k
1
vote
0
answers
2.4k
views
0
answers
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 4.0 years ago by k.nirmalraman900
7
votes
0
answers
2.4k
views
5 follow
0
answers
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 4.0 years ago by k.nirmalraman900
0
votes
1
answer
4.6k
views
1
answers
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 4.0 years ago by k.nirmalraman900
7
votes
1
answer
4.6k
views
6 follow
1
answer
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 4.1 years ago by k.nirmalraman900 • updated 4.0 years ago by Charles Warden4.9k
0
votes
1
answer
3.5k
views
1
answers
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 4.2 years ago by k.nirmalraman900
1
vote
1
answer
3.5k
views
1
answer
Is It Valid To Convert A Fold Change Matrix Into Z Score?
... Dear All, As an assay output we measure expression of one gene per well in a 96 well cell culture plate at different time points/conditions. Eventually, what we have is a matrix (genes x conditions) of gene expression values and we compute the fold change when compared to the control condition. We ...
written 4.2 years ago by k.nirmalraman900 • updated 4.2 years ago by Sean Davis24k

Latest awards to k.nirmalraman

Great Question 10 months ago, created a question with more than 5,000 views. For Deseq: Multiple Conditions Testing
Great Question 3.5 years ago, created a question with more than 5,000 views. For Deseq: Multiple Conditions Testing
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Rna Seq Cell Type Specificity
Great Question 3.5 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?
Great Question 3.5 years ago, created a question with more than 5,000 views. For Gene Expression Data Hierarchical Clustering, Plot Heat Map With Ggplot
Great Question 3.5 years ago, created a question with more than 5,000 views. For Scatter Plot For Correlations With Heatdensity
Great Question 3.5 years ago, created a question with more than 5,000 views. For Bowtie & Tophat
Epic Question 3.5 years ago, created a question with more than 10,000 views. For Scatter Plot For Correlations With Heatdensity
Popular Question 3.5 years ago, created a question with more than 1,000 views. For How Can I Find Position Specific Weight Matrix From A Multi Fasta File
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Mouse Genome Build And Gtf Conflict In Tophat Downloads
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Fasta Length
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Circos: Plotting Various Transcripts Of A Gene?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Deseq: Multiple Conditions Testing
Great Question 3.5 years ago, created a question with more than 5,000 views. For How To Transform From Rna-Seq Deseq To Limma Voom() And Makecontrasts
Popular Question 3.5 years ago, created a question with more than 1,000 views. For How To Generate A Smaller, Simpler Heatmap Similar To A Tile?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Visualizing Bowtie Output In Genome Browser
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Counting Features In A Bed File
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Marker Based Classification Of Expression Data
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Tophat - Htseq Count? How Can I Improve The Mapping Percentage For Single End Reads
Popular Question 3.5 years ago, created a question with more than 1,000 views. For 3' Rna Seq Pipeline
Popular Question 3.5 years ago, created a question with more than 1,000 views. For How To Get Annotation For Bed File From Another Bed File
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Cell Type Composition In A Tissue Based On Gene Marker Expression
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Can We Compare Two Different Rna-Seq Experiments?
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Sequence Logos With Weblogo Scale

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 711 users visited in the last hour