User: EpiExplorer

gravatar for EpiExplorer
EpiExplorer70
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New Zealand
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Posts by EpiExplorer

<prev • 44 results • page 1 of 5 • next >
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PCA plot for methylated fragments
... Hi I would like to create a PCA plot on samples to see how 15 samples in my data group based on the methylation profile of common methylated fragments ? I have data for 400,000 common methylation fragments for each sample. I have transposed the file now in such a way that there are 15 rows represen ...
sequencing written 15 months ago by EpiExplorer70
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Answer: A: How to do gene enrichment analysis using only GO-slim terma
... You can try PANTHER Gene List Analysis and choose Panther Go Slims in the annotations drop down (http://www.pantherdb.org). Let me know how you go. Good Luck. ...
written 19 months ago by EpiExplorer70
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Comment: C: fpkm to tpm conversion
... Hi Which package do I need to install for this code? ...
written 19 months ago by EpiExplorer70
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genes upstream or downstream of a LNcRNA
... Hi I have the list of LncRNAs of interest and their coordinates in BED format. I am interested in identifying the protein coding genes that are 300kb upstream and 300kb downstream of each of those LncRNAs. The genome annotation of lncRNA is gencode 27. I would like to how I can find the upstream/do ...
rna-seq written 19 months ago by EpiExplorer70
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Comment: C: Co-expression network using Cytoscape
... [enter link description here][1] First column has LncRNAs IDs, next 5 columns have correlation values between each LncRNA across 5 different genes in the 5 columns. Image link is below:![enter image description here][2] Sorry I am unable to send the link for some reason. ...
written 19 months ago by EpiExplorer70
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Comment: C: Co-expression network using Cytoscape
... Hi Wietje, Thanks for the answer. I am new to Cytoscape so my next question may sound stupid. The text file I have have the LncRNAs in first column and the other columns consist of header name as gene names and value in those columns the values as correlation values. Now since the file I have is k ...
written 19 months ago by EpiExplorer70
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Co-expression network using Cytoscape
... Hi I have mrNA expression and LncRNA expression data from RNASeq. I have calculated the correlation analysis between the differentially expressed genes and the differentially expressed LnCRNAs. I am interested to visualise the correlation matrix in form of co-expression network using Cytoscape. I ...
rna-seq written 19 months ago by EpiExplorer70 • updated 19 months ago by Wietje210
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TCGA SKCM- How to identify groups in RNA-Seq data
... How to cluster TCGA data with a defined set of genes, in order to classify TCGA data? I have a set of differentially expressed genes in from my analysis using melanoma cell lines from two melanoma sub-types which are independent of tumour stage and disease stage. Now I would like to see how my lis ...
rna-seq written 20 months ago by EpiExplorer70
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Comment: C: Filter by Fold change in DESeq2
... Thank you for your reply. But this is not I want. ...
written 2.9 years ago by EpiExplorer70
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Comment: A: Filter by Fold change in DESeq2
... Hi, I need urgent help in this please. I have read the vignette but I am not clear how to get the genes that are significant with 5% FDR and also greater than or equal to fold change of -2/+2. I have the list of genes which was extracted by results function with alpha value as 0.05. Now if I want t ...
written 2.9 years ago by EpiExplorer70

Latest awards to EpiExplorer

Popular Question 6 months ago, created a question with more than 1,000 views. For How to get per sample read counts/FPKM values from cufflinks?
Great Question 12 months ago, created a question with more than 5,000 views. For Unable to find Bowtie2 index
Popular Question 12 months ago, created a question with more than 1,000 views. For Nimblegen DMA methylation microarray data analysis
Student 12 months ago, asked a question with at least 3 up-votes. For Filter by Fold change in DESeq2
Popular Question 19 months ago, created a question with more than 1,000 views. For RABT by cufflinks
Popular Question 19 months ago, created a question with more than 1,000 views. For How to get per sample read counts/FPKM values from cufflinks?
Popular Question 19 months ago, created a question with more than 1,000 views. For Human genome build
Popular Question 2.9 years ago, created a question with more than 1,000 views. For How to get per sample read counts/FPKM values from cufflinks?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For How does Trimmomatic work?
Popular Question 2.9 years ago, created a question with more than 1,000 views. For Unable to find Bowtie2 index
Popular Question 4.0 years ago, created a question with more than 1,000 views. For How does Trimmomatic work?
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Unable to find Bowtie2 index
Scholar 4.0 years ago, created an answer that has been accepted. For C: RABT by cufflinks

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