User: dsp

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dsp60
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Posts by dsp

<prev • 60 results • page 1 of 6 • next >
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subclass mapping algorithm for subclassing independent datasets
... I went through a paper "Subclass Mapping: Identifying Common Subtypes in Independent Disease Data Sets" (http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0001195) which is used for classification. Is there anyone who used this? Is there any R code available to produce the classifica ...
bioinformatics submap classification cancer written 21 days ago by dsp60
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Comment: C: How to identify DE lncRNA from RNA Seq Data?
... Ok. So from the Count matrix with genes and Samples I remove the pcRNA genes based on lncRNA annotation(Gencode or Ensembl), I have only lncRNAs for the normalization and DE analysis steps. Am I right? ...
written 4 weeks ago by dsp60
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Comment: C: How to identify DE lncRNA from RNA Seq Data?
... @EagleEye I have another doubt. In your previous comment If I want to do in the other way like before normalization if I remove the pcRNAs and take only lncRNAs then do the normalization, Will dis be right way? And Could you please tell me where I can get the annotation only for lncRNAs? Thank you ...
written 4 weeks ago by dsp60
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Comment: C: How to identify DE lncRNA from RNA Seq Data?
... Yes, Thank you very much. I gt the point and dis makes sense. ...
written 4 weeks ago by dsp60
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Comment: C: How to identify DE lncRNA from RNA Seq Data?
... Yes, I can do it from the beginning but I would like to know whether doing the other way is right or not? Could you please tell me about that. Thank you ...
written 4 weeks ago by dsp60
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Comment: C: How to identify DE lncRNA from RNA Seq Data?
... Thank you. But the Mapping is already done with ref genome with total RNA's already. Now I have DE genes and their annotation too. So, If I have lncRNA annotation now I can filter from that right? Do you think this is fine? ...
written 4 weeks ago by dsp60
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How to identify DE lncRNA from RNA Seq Data?
... Hello Everyone, The Data I'm using is Count based. I used DESeq2 to find differential expressed genes between two Groups, Cancer and Normal. I want to identify Long non coding RNA's from these. Can anyone please tell me how can I go forward in this analysis? Thank you ...
rna-seq lncrna written 4 weeks ago by dsp60
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Comment: C: How to perform Fisher's exact test between two gene lists for a particular gene
... For eg: I want see for MAP3K1. Could you please tell how to see it is wildtype or mutant? And then after that I want to perform fisher.test function. MAP3K1 wt mutant Genelist1 x x Genelist2 x x ...
written 10 weeks ago by dsp60
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How to perform Fisher's exact test between two gene lists for a particular gene in R?
... Hello Everyone, I have two gene lists with sample, gene, chromosome, mutation_type, start, end, codon columns. Want to perform Fishers test between two gene lists for a particular gene eg: MAP3K1. Can anyone tell me how can I perform this in R? Thank you ...
R test fishers significance statistics written 10 weeks ago by dsp60 • updated 10 weeks ago by sysbiocoder150
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Comment: C: How to create a mutation landscape (waterfall) plot with GenVisR
... Hi Rahel, The link which you posted is not working. If you want to give an image Go to (https://imgsafe.org/) and browse the image u need, copy the link. Above the comment box, click the image and Paste the link you copied before. Better create a new question. Thank you ...
written 10 weeks ago by dsp60

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