User: Ron

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Ron600
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3 years, 7 months ago
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Posts by Ron

<prev • 274 results • page 1 of 28 • next >
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Confirming Viruses detected from NGS data
... Hi all, I found Oncogenic viruses using VirusSeq (http://odin.mdacc.tmc.edu/~xsu1/VirusSeq.html )in some of the RNA-seq HUMAN samples.However I want to view the evidence of these virus reads in IGV. Should I just align the human RNA-seq to virus genome ,get the bam using STAR and load the bam fi ...
ngs rna-seq virus written 6 weeks ago by Ron600 • updated 6 weeks ago by swbarnes22.8k
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Comment: C: Detection of fusion events of Retrotransposons and genes/lncRNA from RNA-seq dat
... Usually I use Junction Reads > 2 and Spanning Pairs > 1 for fusions with good support. Although there could be novel fusions with only Junction Reads or only Spanning Pairs . ...
written 8 weeks ago by Ron600
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MA plot from Differential Expression between One Sample vs another
... Hi all, Is it possible to get MAplots when you only have foldchange and Expression values of the two samples of comparison(one vs one) ? I don't have replicates.So i only have FPKMS from 2 samples and their log2FoldChange.I know I don't have statistical significance but I still would like to have M ...
R bioconductor differential-expression rna-seq written 10 weeks ago by Ron600
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Motifs from mutations in RNAseq
... Hi all, I am doing mutation analysis on RNAseq using rnaseqmut ( https://github.com/davidliwei/rnaseqmut ) .Is there any way to annotate mutations with the actual motifs? I want to look if some mutations lie in specific motifs of interest e.g. CCAUCG Thanks, Ron ...
mutation rna-seq written 3 months ago by Ron600
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Answer: A: Softwares for Bacterial/Viral Classification from RNAseq
... VirusFinder: Software for Efficient and Accurate Detection of Viruses and Their Integration Sites in Host Genomes through Next Generation Sequencing Data I came across this software and its easy to install compared to the others,and it gives good results. e.g. I had some samples positive for viruse ...
written 4 months ago by Ron600
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Comment: C: Deconvolution methods on RNAseq data
... Are you still working on getting LM22 signature? ...
written 4 months ago by Ron600
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Comment: C: trinitry Virusfinder error message no contigs
... Were you able to find the older version of Trinity? ...
written 4 months ago by Ron600
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Silhouette plots in R
... Hi all, I want to create Silhouette plots in R. I have the code for that: library (cluster) library (vegan) dis = vegdist(exp_matrix) res = pam(dis,3) #choice of clustering algorithm sil = silhouette (res$clustering,dis) # cluster vector pdf('my_nice_plot.pdf') plot( ...
R silhouette clustering rna-seq written 4 months ago by Ron600 • updated 4 months ago by Mattias Aine410
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Comment: C: Detecting isoforms in raw counts (or FPKM) after htseq-count
... You can get isoforms expression from Cufflinks in the isoforms.fpkm_tracking file. ...
written 5 months ago by Ron600
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Comment: C: CAGE seq & RNA-seq
... I just want to use FANTOM data which has different cell types and do clustering analysis with regular RNAseq data based on Expression levels.Has anybody done this kind of analysis ? I am not interested in the primary purpose served by CAGE,thats what I mean.Since FANTOM has multiple cell types Exp ...
written 5 months ago by Ron600

Latest awards to Ron

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Database of Ligand and receptor genes
Student 12 weeks ago, asked a question with at least 3 up-votes. For GSEA Preranked analysis on RNA-SEQ
Popular Question 3 months ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: pca analysis for differential gene expression data of microarray samples of simi
Popular Question 5 months ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Great Question 5 months ago, created a question with more than 5,000 views. For GSEA Preranked analysis on RNA-SEQ
Popular Question 5 months ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Popular Question 6 months ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
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Popular Question 7 months ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Popular Question 8 months ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Popular Question 10 months ago, created a question with more than 1,000 views. For Rank Genes By FPKM for only One Sample
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: pca analysis for differential gene expression data of microarray samples of simi
Popular Question 11 months ago, created a question with more than 1,000 views. For Rank Genes By FPKM for only One Sample
Popular Question 13 months ago, created a question with more than 1,000 views. For Cufflinks output with filename prefix
Popular Question 13 months ago, created a question with more than 1,000 views. For Clustering of genes using FPKM
Popular Question 14 months ago, created a question with more than 1,000 views. For htseq-count for RNA Seq
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Popular Question 17 months ago, created a question with more than 1,000 views. For GSEA for RNASEQ
Popular Question 17 months ago, created a question with more than 1,000 views. For Extracting reads from multiple regions
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Popular Question 19 months ago, created a question with more than 1,000 views. For GSEA for RNASEQ
Popular Question 21 months ago, created a question with more than 1,000 views. For GSEA for RNASEQ
Popular Question 22 months ago, created a question with more than 1,000 views. For GSEA Preranked analysis on RNA-SEQ
Popular Question 22 months ago, created a question with more than 1,000 views. For GSEA Preranked analysis on RNA-SEQ

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