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Right now all config files in `configs/` directory are tab-delimited files. It is not very friendly to work with. For example, it's very easy to confuse `tab` delimiter with space characters.
Two …
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To whom, it may concern.
I would like to run the same pipeline used to generate Recount2 in my dataset.
To check if the rail-RNA pipe worked correctly I ran it on a small project uploaded in Recoun…
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Hello,
I am usually a happy camper with `recount2` and very thankful for all the work you all have put into this tool! That being said, I have noticed a bug recently in which using the `RangedSumma…
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Hello!
When trying to access the RAIL server from Recount2, I got an error. Here is the link: http://duffel.rail.bio/recount/v2/SRP025982/rse_gene.Rdata
Here is the error:
 when we are querying GTEX?
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I downloaded liver RNA-seq processed data from GTEx by using TCGAquery_recount2, and I got a returned object called liver.rec.I want to know the detail about colnames of liver.rec,but I don't know how…
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Hello,
I installed the EQP-cluster as per the instructions & it seems to have installed without any problems (creation of Bowtie2 indices completed).
When I attempt to use Split though (./proc…
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In this function:
https://github.com/greenelab/ponyo/blob/60f00701cf6cf54e92c88ee2100846ed575ed08f/ponyo/simulate_expression_data.py#L421-L431
the first argument is the filename of normalized data.…
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At BioC2019 @sonali-bioc requested having a function for loading multiple RSE files.
This is just a reminder to myself for actually doing this :-)
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The current `get_sample_ids` function, used by the experiment-level simulations (i.e. `simulate_by_latent_transformation` and `shift_template_experiment`), assumes that the user is using one of two di…