User: greg.mulhearn

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Posts by greg.mulhearn

<prev • 9 results • page 1 of 1 • next >
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Comment: C: DEXSeq - Where to find and download the appropriate GTF reference file for Pytho
... Thanks James.  I have been away for a week or so, but have been able to successfully follow through the processes in your answer, and everything worked well.  We used the GTF file:  Drosophila_melanogaster.BDGP5.78.gtf (loaded using the command   z <- hub[["AH28596"]] ) However, we now have a ne ...
written 10 weeks ago by greg.mulhearn0
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Comment: C: DEXSeq - Where to find and download the appropriate GTF reference file for Pytho
... Thanks for that James. However, I have run in to another problem. When I went back in to R (actually I'm using RStudio on a Windows PC), and tried to re-run all the commands in your initial solution steps, I successfully completed the first command ( library(AnnotationHub) ).  However, when I enter ...
written 12 weeks ago by greg.mulhearn0
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Comment: C: DEXSeq - Where to find and download the appropriate GTF reference file for Pytho
... Thanks James for your reply.  I have followed your detailed instructions above and from looking at the resultant object, it looks like this will solve our problem. However, when I get to the last step within "R"  (> export(z, "tmp.gtf", "gtf")), I get the message: Error: could not find function ...
written 12 weeks ago by greg.mulhearn0
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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 3 months ago by greg.mulhearn0 • updated 3 months 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 2.2 years ago by greg.mulhearn0 • updated 2.2 years 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 2.2 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 2.2 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 2.2 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 2.2 years ago by greg.mulhearn0

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Popular Question 2.2 years 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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