User: Vasu

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Vasu490
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Posts by Vasu

<prev • 295 results • page 1 of 30 • next >
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Answer: A: Gene Ontology using clusterProfiler
... data <- c("FAP","COL10A1","ADAM12","POSTN") library(clusterProfiler) library(org.Hs.eg.db) ### Convert UpReg Gene symbols to Ensembl ids and Entrez ids Ent_Ensem_UNI <- bitr(data, fromType = "SYMBOL", toType = c("ENTREZID", "ENSEMBL", "UNIPR ...
written 4 months ago by Vasu490
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Answer: A: Pathway/Gene set z-score from log2FC
... you can go with `fgsea` to do Gene set enrichment analysis. check this tutorial [DESeq results to pathways in 60 Seconds with the fgsea package][1] [1]: https://stephenturner.github.io/deseq-to-fgsea/ ...
written 4 months ago by Vasu490
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Comment: C: RNA seq data analysis and building co expression network
... For your first question - I recommend you to check [edgeR][1] or [deseq2][2] The second question - you can use `WGCNA` R package for co-expression network analysis. you have to use normalized data like log2(counts+1) or FPKM, logCPM data as input. [1]: https://www.bioconductor.org/packages/re ...
written 4 months ago by Vasu490
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Comment: C: Question about WGCNA Module Eigengenes to Pathway analysis
... one help again. datKME=signedKME(datExpr, mergedMEs) FilterGenes= abs(datKME$kMEgreen)>0.8 table(FilterGenes) FilterGenes FALSE TRUE 14006 1019 dimnames(data.frame(datExpr))[[2]][FilterGenes] When I used like above to get the hub genes from module `gree ...
written 5 months ago by Vasu490
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Comment: C: Question about WGCNA Module Eigengenes to Pathway analysis
... yes just now found that and I thought of doing this. thanks a lot. ...
written 5 months ago by Vasu490
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Comment: C: Question about WGCNA Module Eigengenes to Pathway analysis
... thanks and I have a small question. I'm able to get the hub genes from the modules before merging i.e. from 34 modules. But I would like to know how to get the hub genes from the merged modules i.e. 17 modules. How to do it? The below code gave me hub genes from one of the modules before merging. ...
written 5 months ago by Vasu490
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Question about WGCNA Module Eigengenes to Pathway analysis
... I have a very basic question for co-expression network analysis. I'm using WGCNA. I got 34 modules as output. After this, I calculated their eigengenes and clustered them on their correlation into 17 modules. My question - Can I use the genes from the merged modules for pathway analysis? or do I ...
wgcna geneexpression coexpressionnetwork rna-seq written 5 months ago by Vasu490 • updated 5 months ago by andres.firrincieli970
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Comment: C: Different miRNAs with same miRNA regions in TCGA
... Ok got the answer from this link [miRNAseq isoform-to-mature miRNA quantification][1] [1]: https://www.biostars.org/p/101182/ ...
written 12 months ago by Vasu490
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Comment: C: Different miRNAs with same miRNA regions in TCGA
... In `mirTarbase` hsa-let-7a-5p is the only which has Accession `MIMAT0000062`. I actually want the names of the above table and miRNA target information names to be same. And this can be only based on `miRNA_region`. So, if I treat all the three miRNAs like that it will be same miRNA region for all t ...
written 12 months ago by Vasu490
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Different miRNAs with same miRNA regions in TCGA
... I have the miRNA data from TCGA as below: where for three miRNAs have the same mature miRNA region. Should I treat all of them as the same miRNA? I mean can I sum the read counts based on the miRNA region and treat all as single miRNA? miRNA_ID read_count miRNA_region barcode hsa-let-7a-1 ...
mirtarbase tcga mirnaseq mirna written 12 months ago by Vasu490

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Popular Question 10 weeks ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Great Question 3 months ago, created a question with more than 5,000 views. For Sample names for TCGA data from GDC-legacy archive
Popular Question 3 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Great Question 11 months ago, created a question with more than 5,000 views. For Sample names for TCGA data from GDC-legacy archive
Popular Question 11 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 11 months ago, created a question with more than 1,000 views. For cuffdiff for groups
Popular Question 11 months ago, created a question with more than 1,000 views. For error after running tophat
Popular Question 11 months ago, created a question with more than 1,000 views. For Sample names for TCGA data from GDC-legacy archive
Popular Question 11 months ago, created a question with more than 1,000 views. For Bam to read counts for differential expression analysis
Popular Question 11 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
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Student 13 months ago, asked a question with at least 3 up-votes. For Sample names for TCGA data from GDC-legacy archive
Popular Question 13 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Good Answer 15 months ago, created an answer that was upvoted at least 5 times. For C: Sample names for TCGA data from GDC-legacy archive
Popular Question 15 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 15 months ago, created a question with more than 1,000 views. For cuffdiff for groups
Popular Question 16 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
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Popular Question 18 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
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Popular Question 20 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 20 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot
Popular Question 20 months ago, created a question with more than 1,000 views. For cuffdiff for groups
Popular Question 23 months ago, created a question with more than 1,000 views. For Reading Affymetrix data from pd.hugene.2.0.st using oligo for RNA degradation plot

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