User: prakash

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prakash240
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Posts by prakash

<prev • 49 results • page 1 of 5 • next >
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Comment: C: Multiple transcripts for same gene in array gene expression profile?
... May be you can take average of expression of all the transcript as gene expression. ...
written 1 day ago by prakash240
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Comment: C: Correlation of TF Binding with expression data
... Thanks Venu ! I have ChIPseq data for TF in control and KD condition. I have annotated the TFBS/peak to nearest genes using homer (default it annotates to only one nearest gene) and have normalized tag count as well. Each binding site can be correlated with expression, but what you would do if you ...
written 2 days ago by prakash240
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Correlation of TF Binding with expression data
... Hi, I would like to perform correlation analysis between gene expression and TF binding in control and KD condition. So what I have till now is gene expression in control and KD condition and normalized tag count of different transcription factor obtained from Homer annotatePeaks.pl for merged peak ...
chip-seq rna-seq written 2 days ago by prakash240 • updated 2 days ago by venu5.5k
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Answer: A: annotatePeaks.pl without annotation in genes name
... In Homer, there is annotatePeaks.pl which annotates the peak to nearest gene ...
written 9 days ago by prakash240
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Comment: C: Connect gene names to GO terms/function for loading in DESeq2
... The link you tried will only provide enriched GO terms for you set of genes, basically it compares your set of genes against respective databases and calculates enrichment and significance. providing only one gene will not return anything. If you really interested in only GO annotation, then you sh ...
written 17 days ago by prakash240
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Answer: A: Connect gene names to GO terms/function for loading in DESeq2
... In Figure D , what they have shown is enriched GO terms for 363 AKT differentially expressed genes. GO terms and DESeq2 analysis are two different things. you can find enriched GO terms for whole set of gene but that would be very less meaningful. I would rather first go for differential expression ...
written 17 days ago by prakash240
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Answer: A: hierarchical clustering heat map to RNAseq data
... May be you can try [Shinyheatmap][1] [1]: http://shinyheatmap.com/ ...
written 17 days ago by prakash240
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Comment: A: GSEA top genes vs all platform
... Have a loot at this [thread][1], may be helpful [1]: https://www.biostars.org/p/279097/ ...
written 19 days ago by prakash240
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Answer: A: How to convert transcript level TPM to gene level TPM ?
... To convert gene count to TPM , you can use this [R script][1] and to get gene level TPM from transcript. [1]: https://gist.github.com/slowkow/c6ab0348747f86e2748b ...
written 19 days ago by prakash240
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Comment: C: Bedsect: An integrated web server application to perform intersection, visualiza
... Well, Galaxy is indeed a great platform that provides users to select tools to perform specific task. In case of BED files overlap, multiple other analyses can be performed like functional annotation of intersecting regions locating regions in genome browsers for and extracting regions for primer de ...
written 22 days ago by prakash240

Latest awards to prakash

Appreciated 16 days ago, created a post with more than 5 votes. For A: Gene Set Enrichment Analysis after DESeq2
Appreciated 26 days ago, created a post with more than 5 votes. For A: Gene Set Enrichment Analysis after DESeq2
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Finding instances of motifs near peaks
Scholar 10 months ago, created an answer that has been accepted. For A: Gene Set Enrichment Analysis after DESeq2
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Gene Set Enrichment Analysis after DESeq2
Popular Question 10 months ago, created a question with more than 1,000 views. For how to get p value for a set of fdr value
Popular Question 12 months ago, created a question with more than 1,000 views. For how to get p value for a set of fdr value

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