User: bharata1803

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bharata1803280
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Japan
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Posts by bharata1803

<prev • 198 results • page 1 of 20 • next >
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Comment: C: Salmon choosing library type
... the automatic result has quite good mapping rate and most of the sample is detected as unstranded. so I think I will ust set it to automatic then. ...
written 8 weeks ago by bharata1803280
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Salmon choosing library type
... Hello, So, I try to use salmon to quantify the read count from my fastq. I use salmon quant for this method. My question is how can I determine the library type? I know salmon provide automatic lib type detection, but I just want to make sure to choose the right lib type. From the GEO dataset, the ...
alignment salmon written 8 weeks ago by bharata1803280 • updated 8 weeks ago by igor6.5k
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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 5 months ago by bharata1803280
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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 8 months ago by bharata1803280
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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 8 months ago by bharata1803280
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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 8 months ago by bharata1803280 • updated 8 months ago by Leite300
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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 8 months ago by bharata1803280
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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 8 months ago by bharata1803280
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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 9 months ago by bharata1803280
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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 9 months ago by bharata1803280

Latest awards to bharata1803

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 Alternative sequence gene Ensembl ID
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)
Popular Question 5 months ago, created a question with more than 1,000 views. For Comparison of microarray and RNA-seq data
Popular Question 5 months ago, created a question with more than 1,000 views. For Salmon warning detected suspicious pair
Popular Question 5 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
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Popular Question 7 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 7 months ago, created a question with more than 1,000 views. For Microarray and RNA-seq different result
Popular Question 8 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 8 months ago, created a question with more than 1,000 views. For Microarray and RNA-seq different result
Popular Question 8 months ago, created a question with more than 1,000 views. For About logFC and p-value( and adj p-value)
Popular Question 8 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 9 months ago, created a question with more than 1,000 views. For JASPAR motifs download
Popular Question 9 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 9 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 11 months ago, created a question with more than 1,000 views. For Download human 3 UTR FASTA file
Popular Question 11 months ago, created a question with more than 1,000 views. For Microarray and RNA-seq different result
Popular Question 11 months ago, created a question with more than 1,000 views. For About logFC and p-value( and adj p-value)
Popular Question 13 months ago, created a question with more than 1,000 views. For About logFC and p-value( and adj p-value)
Popular Question 14 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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