User: DataFanatic

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DataFanatic110
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Posts by DataFanatic

<prev • 77 results • page 1 of 8 • next >
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Comment: C: where to keep scripts for new software
... Yes,I apologize if this is not within the bioinformatics subject, but it is certainly a fundamental (basic but fundamental) concept also used in bioinformatics. How can one create a symlink from $HOME/path/to/package to $HOME/bin Thank you!! ...
written 14 days ago by DataFanatic110
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where to keep scripts for new software
... When downloading software in a unix system to a bin directory $HOME/bin a new directory containing the scripts is created $HOME/bin/packagedir adding this to the path everytime you download a new package makes the $PATH long and complicated. Would you advice to transfer all the scripts from the or ...
$path install unix written 14 days ago by DataFanatic110
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Comment: C: Pacbio inversion visualization and IGV
... Picasa , Did you figure this out? ...
written 28 days ago by DataFanatic110
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Comment: C: GMAP download page
... Thank you for your answer, Yes I am referring to GMAP. Let me clarify my second question: I only have a PC/Mac **and** **no** Unix server. Can I install SMRTLink on my Mac/PC?? Also, is GMAP a good alternative to SMRTLink? I need to detect gene isoforms without a reference. ...
written 28 days ago by DataFanatic110
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GMAP download page
... I am interested in analyzing PacBio long read (full transcript) RNAseq data using GMAP; however, GMAP download page seems to have been removed. Does anyone know if GMAP is still available for download? PacBio have their own software SMRTlink software but I believe this will not run on windows or mac ...
gmap rna-seq pacbio written 28 days ago by DataFanatic110
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Answer: A: differential gene expression analysis
... Devon, How can I plot the data going into the analysis? design<-model.matrix(~group+batch+RIN) will include RIN in the model and this should change the way samples cluster by PCA or MDS plot. Is there a way to extract the corrected counts matrix? Thank you! ...
written 5 months ago by DataFanatic110
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Comment: A: differential gene expression analysis
... Is there a way to visualize the data (residuals) using PCA or MDS plot after performing the linear modeling? I want to do this to confirm the samples no longer cluster by batch. ...
written 5 months ago by DataFanatic110
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Comment: A: differential gene expression analysis
... "Yes, typically one simply adds batch and RIN as covariates if they seem relevant. " Do you mean that you can add covariates into the model matrix e.g. design<-model.matrix(~group+batch+RIN) Thanks! ...
written 5 months ago by DataFanatic110
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differential gene expression analysis
... I'm trying to do differential gene expression analysis (RNA-Seq data) using Limma and EdgeR How can I adjust my count matrix for technical confounders(RIN, batch)? a. Is it possible to adjust for confounders within Limma? b. Can I adjust the count matrix for covariates using linear regression and ...
confounders edger limma rna-seq regression written 5 months ago by DataFanatic110
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missing a sample and individual attributes in GTEX Adipose- Subcutaneous(v7)
... I'm working with GTEx Adipose- Subcutaneous(v7) and have several missing sample and individual attributes in the GTEx Subcutaneous Adipose, specifically: Adipose - Subcutaneous=294 samples in the genotype file Adipose - Subcutaneous=294 samples in the expression values When subsetting the indi ...
adipose rna-seq gtex written 8 months ago by DataFanatic110

Latest awards to DataFanatic

Supporter 12 months ago, voted at least 25 times.
Popular Question 17 months ago, created a question with more than 1,000 views. For merging two bigwig files

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