User: Ron

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Ron580
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580
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3 years, 5 months ago
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Posts by Ron

<prev • 272 results • page 1 of 28 • next >
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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 7 days ago by Ron580
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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 6 weeks ago by Ron580
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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 10 weeks ago by Ron580
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Comment: C: Deconvolution methods on RNAseq data
... Are you still working on getting LM22 signature? ...
written 10 weeks ago by Ron580
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Comment: C: trinitry Virusfinder error message no contigs
... Were you able to find the older version of Trinity? ...
written 11 weeks ago by Ron580
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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 12 weeks ago by Ron580 • updated 11 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 3 months ago by Ron580
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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 3 months ago by Ron580
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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 3 months ago by Ron580
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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 3 months ago by Ron580 • updated 3 months ago by Santosh Anand2.3k

Latest awards to Ron

Student 21 days ago, asked a question with at least 3 up-votes. For GSEA Preranked analysis on RNA-SEQ
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Teacher 10 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 12 weeks ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Great Question 3 months ago, created a question with more than 5,000 views. 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
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 6 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 Rank Genes By FPKM for only One Sample
Teacher 8 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 9 months ago, created a question with more than 1,000 views. For Rank Genes By FPKM for only One Sample
Popular Question 11 months ago, created a question with more than 1,000 views. For Cufflinks output with filename prefix
Popular Question 11 months ago, created a question with more than 1,000 views. For Clustering of genes using FPKM
Popular Question 12 months ago, created a question with more than 1,000 views. For htseq-count for RNA Seq
Centurion 12 months ago, created 100 posts.
Popular Question 15 months ago, created a question with more than 1,000 views. For GSEA for RNASEQ
Popular Question 15 months ago, created a question with more than 1,000 views. For Extracting reads from multiple regions
Student 15 months ago, asked a question with at least 3 up-votes. For GSEA Preranked analysis on RNA-SEQ
Popular Question 17 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 for RNASEQ
Popular Question 20 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
Popular Question 21 months ago, created a question with more than 1,000 views. For GSEA Preranked analysis on RNA-SEQ

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