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Update the following URL to point to the GitHub repository of
the package you wish to submit to Bioconductor
```
Repository: https://github.com/leekgroup/recount
```
Confirm the following by editing…
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Hi,
I am using derfinder to compare two groups of samples (31 vs 17) and I want to optimize (and understand) my statistics. However, it is not clear to me how this is built in analyzeChr().
As it i…
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It would be useful to speed up the p-value calculation step.
One quick solution would be to round the areas a bit, then find the p-values for the unique areas and then assign them to each candidate …
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Can the analysis in the paper [Differential expression analysis of RNA-seq data at single-base resolution](http://biostatistics.oxfordjournals.org/content/early/2014/01/06/biostatistics.kxt053.full) b…
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I got this `makeDb` error when running `analysis_code.R`:
```
> makeDb(dbfile = dbfile, tablename = tablename, textfile = textfile, cutoff = 5)
Error in if (.allows_extensions(db)) { :
missing val…
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Hullo
I am trying to use derfinder to find differentially enriched regions in some human histone mark chip-seq data. I have bam files that were created with STAR and indexed with samtools. I have an…
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When trying to run `analysis_code.R`, the "chunk 3a: load resuls from Cufflinks" section gives missing file errors because the `*cuff-UDPATED.rda` files are missing:
- https://github.com/alyssafrazee/…
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In your [README.md](https://github.com/alyssafrazee/derfinder/blob/master/README.md), you mention `locfdr` in the installation section. Since `locfdr` has been [removed from CRAN](http://cran.r-projec…
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I'm seeing weird results in Snyder and Hippo when reproducing the results from last year.
# Hippo
New:
![new](https://cloud.githubusercontent.com/assets/2288213/5145458/f780c702-7170-11e4-90ec-03cfa1…
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When trying to reproduce results in the 2013 paper, from this code in [analysis_code.R](https://github.com/alyssafrazee/derfinder/blob/master/analysis_code.R) ...
```
# get the flags:
exons = getAnno…