User: Ron

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Ron510
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510
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Posts by Ron

<prev • 266 results • page 1 of 27 • next >
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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 6 days ago by Ron510
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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 6 days ago by Ron510
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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 6 days ago by Ron510
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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 7 days ago by Ron510 • updated 6 days ago by Santosh Anand840
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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 21 days ago by Ron510
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RNAseq analysis of FFPE samples
... Hi all, I wanted to know what kind of QC checks can be done for RNA access samples so that can be used for analysis ,similar to regular RNAseq data sequenced by Truseq kits(polyA). Since RNA access is for low quality RNA FFPE, what analysis can be done to check if we can use the data from them? I ...
next-gen rna-seq sequencing written 5 weeks ago by Ron510
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Comment: C: Installing ABYSS-P from source
... I am using linux,also I cant find the link to the package.Can you send it here? ...
written 5 weeks ago by Ron510
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Installing ABYSS-P from source
... Hi all, I am installing ABYSS,installation works fine. but ABYSS-P is not installed. I have installed open-mpi as well . Is it because of MPI_Init ? Commands to install: ./configure --prefix=/dir --with-mpi=/dir --without-sparsehash make make install checking mpi.h usabili ...
next-gen rna-seq abyss written 5 weeks ago by Ron510 • updated 5 weeks ago by Philipp Bayer4.0k
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Deconvolution methods on RNAseq data
... Hi all, This question is similar to this post. https://www.biostars.org/p/160961/#237546 I have been using CIBERSORT and DeconRNAseq, but both of them give different results. 1. Does anyone know of other cell type signatures besides LM22 from CIBERSORT which has only 22 cell types? Signature ...
R bioconductor next-gen rna-seq sequencing written 5 weeks ago by Ron510 • updated 13 days ago by p.taus100
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Comment: C: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
... Does anyone know of other cell type signatures besides LM22 from CIBERSORT which has only 22 cell types? Also,are there any other tools for RNAseq besides CIBERSORT and DeconRNAseq? ...
written 5 weeks ago by Ron510

Latest awards to Ron

Popular Question 5 days ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Great Question 20 days ago, created a question with more than 5,000 views. 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
Popular Question 4 weeks ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Popular Question 9 weeks ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
Popular Question 11 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 5 months ago, created a question with more than 1,000 views. For Rank Genes By FPKM for only One Sample
Teacher 5 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 6 months ago, created a question with more than 1,000 views. For Rank Genes By FPKM for only One Sample
Popular Question 8 months ago, created a question with more than 1,000 views. For Cufflinks output with filename prefix
Popular Question 8 months ago, created a question with more than 1,000 views. For Clustering of genes using FPKM
Popular Question 9 months ago, created a question with more than 1,000 views. For htseq-count for RNA Seq
Centurion 9 months ago, created 100 posts.
Popular Question 12 months ago, created a question with more than 1,000 views. For GSEA for RNASEQ
Popular Question 12 months ago, created a question with more than 1,000 views. For Extracting reads from multiple regions
Student 12 months ago, asked a question with at least 3 up-votes. For GSEA Preranked analysis on RNA-SEQ
Popular Question 14 months ago, created a question with more than 1,000 views. For GSEA for RNASEQ
Popular Question 16 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 GSEA Preranked analysis on RNA-SEQ
Popular Question 18 months ago, created a question with more than 1,000 views. For GSEA Preranked analysis on RNA-SEQ
Popular Question 18 months ago, created a question with more than 1,000 views. For GSEA Preranked analysis on RNA-SEQ
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