User: Ron

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Ron560
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560
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3 years, 4 months ago
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Posts by Ron

<prev • 271 results • page 1 of 28 • next >
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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 18 days ago by Ron560
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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 6 weeks ago by Ron560
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Comment: C: Deconvolution methods on RNAseq data
... Are you still working on getting LM22 signature? ...
written 6 weeks ago by Ron560
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Comment: C: trinitry Virusfinder error message no contigs
... Were you able to find the older version of Trinity? ...
written 6 weeks ago by Ron560
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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 7 weeks ago by Ron560 • updated 7 weeks ago by Mattias Aine390
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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 8 weeks ago by Ron560
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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 8 weeks ago by Ron560
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Answer: A: abyss-pe without openmpi
... install ABySS using Linuxbrew. See http://linuxbrew.sh Install Linuxbrew, and then brew install homebrew/science/abyss ...
written 8 weeks ago by Ron560
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CAGE seq & RNA-seq
... Hi all, I have read this post on CAGEseq and RNA-seq ,and about the differences in their protocols. https://www.biostars.org/p/155400/ Also,the paper on their comparison which shows they have similar expression profiles: http://genome.cshlp.org/content/early/2014/03/04/gr.156232.113.long Howeve ...
next-gen cage-seq rna-seq written 8 weeks ago by Ron560 • updated 8 weeks ago by Santosh Anand2.2k
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Answer: A: How can I merge two data frames in R with turning one of them?
... Assuming you have expression data in a matrix of gene vs Samples in the second table Use melt function from reshape library to get the data in 3 columns format,which will be gene,Sample,Expression Value library(reshape) df2_melt= melt(df2,id="gene") Now you can merge this data with the fir ...
written 10 weeks ago by Ron560

Latest awards to Ron

Teacher 6 weeks 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 8 weeks ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Great Question 10 weeks ago, created a question with more than 5,000 views. For GSEA Preranked analysis on RNA-SEQ
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Popular Question 3 months ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Popular Question 4 months ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Popular Question 5 months ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Popular Question 7 months ago, created a question with more than 1,000 views. For Rank Genes By FPKM for only One Sample
Teacher 7 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 8 months ago, created a question with more than 1,000 views. For Rank Genes By FPKM for only One Sample
Popular Question 10 months ago, created a question with more than 1,000 views. For Cufflinks output with filename prefix
Popular Question 10 months ago, created a question with more than 1,000 views. For Clustering of genes using FPKM
Popular Question 11 months ago, created a question with more than 1,000 views. For htseq-count for RNA Seq
Centurion 11 months ago, created 100 posts.
Popular Question 14 months ago, created a question with more than 1,000 views. For GSEA for RNASEQ
Popular Question 14 months ago, created a question with more than 1,000 views. For Extracting reads from multiple regions
Student 14 months ago, asked a question with at least 3 up-votes. For GSEA Preranked analysis on RNA-SEQ
Popular Question 16 months ago, created a question with more than 1,000 views. For GSEA for RNASEQ
Popular Question 18 months ago, created a question with more than 1,000 views. For GSEA for RNASEQ
Popular Question 19 months ago, created a question with more than 1,000 views. For GSEA Preranked analysis on RNA-SEQ
Popular Question 19 months ago, created a question with more than 1,000 views. For GSEA Preranked analysis on RNA-SEQ
Popular Question 20 months ago, created a question with more than 1,000 views. For GSEA Preranked analysis on RNA-SEQ
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