User: bharata1803

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bharata1803250
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Japan
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Posts by bharata1803

<prev • 196 results • page 1 of 20 • next >
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FIMO score calculation
... Hello, So, I use FIMO for calculating PWM score for a sequence. How does FIMO calculate the score actually? It says it is the log likelihood of the PWM given background. Can anyone give step by step? Suppose I have PWM: A C G T 1 0.2 0.4 0.4 0 2 0.4 0.2 0.4 0 3 0.6 0 0.2 0.2 4 0 1 0 0 5 1 ...
fimo pwm written 12 weeks ago by bharata1803250
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Comment: C: Enrichment analysis for custom set
... No, I mean not the gene set definition, but the gene list that I want to calculate the enrichment. In DAVID, we just need to paste the gene symbol right, but I thought in GSEA, we need to submit gene list that contains not only the gene symbol but also the p-value or TPM or FPKM or something else. ...
written 5 months ago by bharata1803250
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Comment: C: Enrichment analysis for custom set
... I thought GSEA need gene list with p-value, TPM, or FPKM, right? What I want is similar with DAVID, upload a list of genes and can upload background and then do the enrichment analysis. CMIIW ...
written 5 months ago by bharata1803250
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Enrichment analysis for custom set
... Hello, I want to ask if there is an API for doing enrichment analysis by submitting your own set. For example, I have 5 gene set, Set 1, Set 2, ..., Set 5. I have a list of gene, gene A,B,C,D. I want to calculate the enrichment of gene A,B,C,D in the Set 1, Set 2,.., Set 5. I know several API ...
enrichment gene-ontology written 5 months ago by bharata1803250 • updated 5 months ago by Leite220
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Comment: C: Comparing DEG result from different experiment
... Thank you, I just want to make sure it is make sense. I have several times compare DEG analysis using DESeq2 and Limma and edgeR with same dataset and they produce similar result. ...
written 5 months ago by bharata1803250
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Comparing DEG result from different experiment
... Hello all, So I have a simple question. Suppose I download 2 or more dataset from NCBI GEO. Those dataset come from different experiment especially the NGS machine. For example one of them use Illumina and others use Ion Torrent. My first question is, if I calculated each dataset separately for DE ...
rna-seq deg written 5 months ago by bharata1803250
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Comment: C: Comparison of Subsetting gene sets for enrichment analysis
... Well, the definition of better is subjective. For example, from what I have done, I got 80 significant enrichment result if I don't subset the DEG. From these 80, the top rows mostly are just general cell function. The relevant enrichment result that related to cancer is in the middle. But, if I sub ...
written 6 months ago by bharata1803250
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Comparison of Subsetting gene sets for enrichment analysis
... Hello, So, I am working on a method. From this method I can get a small subset of differentially expressed genes. I only get around ~100 genes compared to if I don't use any subsetting metjhod, around ~3000. From this result, I compare the enrichment analysis using Enrichr, DAVID, and other similar ...
enrichment rna-seq written 6 months ago by bharata1803250
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Comment: C: GDC TCGA Metadata no project ID available?
... This is the metadata that I downloaded manually from GDC and then use my own parser: [csv file][1] [1]: https://www.dropbox.com/s/kjkfy9h6j2f6a9y/metadata_gbm.csv?dl=0 ...
written 6 months ago by bharata1803250
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Comment: C: GDC TCGA Metadata no project ID available?
... I see. If it is from GDC, maybe you can compare if you download manually from the portal. You can see whether the project_id exists in the original json format or not, if you still curious though. ...
written 6 months ago by bharata1803250

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Popular Question 9 weeks ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
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Popular Question 4 months ago, created a question with more than 1,000 views. For Microarray and RNA-seq different result
Popular Question 5 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 5 months ago, created a question with more than 1,000 views. For Microarray and RNA-seq different result
Popular Question 5 months ago, created a question with more than 1,000 views. For About logFC and p-value( and adj p-value)
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