User: Ron

gravatar for Ron
Ron500
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500
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United States
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Joined:
3 years, 1 month ago
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r*********@yahoo.co.in

about me

Posts by Ron

<prev • 261 results • page 1 of 27 • next >
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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 2 days ago by Ron500
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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 2 days ago by Ron500
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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 3 days ago by Ron500 • updated 3 days ago by Philipp Bayer3.9k
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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 7 days ago by Ron500
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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 7 days ago by Ron500
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Comment: C: Differences between Counts and FPKMS
... Okay,another thing I wanted to know is that a norm to see such differences(have you guys come across such differences too in the past)? ...
written 9 days ago by Ron500
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Comment: C: Differences between Counts and FPKMS
... So,what should be the result I go with in this case? fold change from FPKMS or fold change from DEseq ? ...
written 9 days ago by Ron500
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Differences between Counts and FPKMS
... Hi all, I have come across a gene, which show a **7 fold increase** in Treatment (3 replicates ) vs Control (3 replicates ),while looking at FPKMS.(Took Mean of treament/Mean of Control to get a foldchange) But doing differential expression(using counts from htseq-count),I am getting a log2foldcha ...
next-gen differential-expression deseq rna-seq written 9 days ago by Ron500 • updated 9 days ago by Rob1.6k
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Comment: C: Getting Warnings When Configuring The Amos Pipeline
... Hi, Were you able to solve this issue? ...
written 16 days ago by Ron500
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Comment: C: Identifying Viral Sequences In Next Generation Sequencing Data
... Hi Pierre, I am doing viral detection on RNAseq data and found this post.Have you used RINS for this purpose?Any thoughts on this software ? I just wanted to know if it has given some kind of results that have been validated, or also confirmed by other methods. ...
written 21 days ago by Ron500

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Popular Question 4 weeks ago, created a question with more than 1,000 views. For Rare Variants From Annotated Vcf File
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