User: greg.mulhearn

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Posts by greg.mulhearn

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DEXSeq - Where to find and download the appropriate GTF reference file for Python Script
... We are using the DEXSeq package and are following the steps in the workflow vignette (“Inferring differential exon usage in RNASeq data with the DEXSeq package”). We initially downloaded the Biconductor “Pasilla” Data Package (at http://bioconductor.org/packages/release/data/experiment/html/pasilla ...
dexseq gff gtf reference genome written 4 days ago by greg.mulhearn0 • updated 3 days ago by James W. MacDonald43k
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Using RNA-Seq Workflow using Real Life FASTQ data - and Mouse Reference Genome
... I am a new user to R and Bioconductor, so please excuse my inexperience. I have installed R (Ver: 3.1.3) and Biconductor (Ver: 3.0)  on a Windows-7, 64-bit system, as per the instructions on the Bioconductor website. I then followed the instructions in the workflow document:  "RNA-Seq workflow: ge ...
deseq2 fastq deseqdataset rnaseqgene reference genome written 23 months ago by greg.mulhearn0 • updated 23 months ago by James W. MacDonald43k
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Answer: A: Plots and Heat Maps not displaying in RGui Window
... Thanks James.  I started a new RGui and typed plot(1:10).  At first nothing appeared to happen.  But then I discovered that it had opened a new window (within the RGui window), but it was behind the window that I was typing in.  When I minimized the window I was typing in, I could see the plot windo ...
written 2.0 years ago by greg.mulhearn0
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Plots and Heat Maps not displaying in RGui Window
... I am working my way through the "RNA-Seq workflow: gene-level exploratory analysis and differential expression" sample workflow using the sample data included in that workflow. I have reached the point where the workflow document shows some graphical output such as PLOTS or HEAT MAPS.  All of the p ...
plot heatmap deseqdataset rnaseqgene graphical written 2.0 years ago by greg.mulhearn0
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Answer: A: Error with "library("GenomicFeatures")" - "there is no package called ‘XML’"
... Thanks James for your prompt reply which has fixed the problem.  I installed XML as per your instructions, and I was able to proceed with the workflow.   Interestingly, when I did the previous step of installing the workflow as per these instructions: > source("http://bioconductor.org/workflow ...
written 2.0 years ago by greg.mulhearn0
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Error with "library("GenomicFeatures")" - "there is no package called ‘XML’"
... I am a new user to Bioconductor and R, so please excuse my inexperience. I installed R and Biconductor (on a Windows-7, 64-bit system), as per the instructions on the Bioconductor website. I am now trying to follow the instructions in the workflow document:  "RNA-Seq workflow: gene-level explorato ...
genomicfeatures xml loadnamespace written 2.0 years ago by greg.mulhearn0

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Popular Question 23 months ago, created a question with more than 1,000 views. For Error with "library("GenomicFeatures")" - "there is no package called ‘XML’"

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