recount3

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Assuming that we do complete the data uploads to AnVIL https://anvilproject.org/, we would then update `recount3` to make sure that it is compatible with the data hosted there if you...

lcolladotor

[Feature Request] Restore information from Matrix Market files in recount3

3

Hi Ben and Kasper, Now we are conducting a project utilizing data from GTEx project. We are particularly interested in the resource presented in recount3 and would like to seek...

jiapeiyuan17

RNAseq datasets unavailable

2

Good afternoon, I am using recount3 for downloading datasets from several studies, but four I am interested in are not available. The four are: SRP226115 SRP237545 SRP238911 SRP103842 I see...

danielemalpetti

recount::getTPM(rse) method

2

## Description of the issue The function _"recount::getTPM(rse)"_ returns the unexpected error message: _'Error: subscript contains invalid names'_. Below, is a reproducible example that I have been using: ``` rse

SoniaRuiz

I was trying to load in the junction data for project "SRP187599" and after regular loading prompt through all of the files I received the error below. I know there...

aobermayer4

[BUG] different row counts implied by arguments error at expand_sra_attributes()

2

## Describe the bug DataFrame dimension mismatch error using data from project SRP017465 ``` rse_expanded

ivokwee

Hi Leonardo, thanks for `recount3`; I was wondering whether there is a hack to produce the `RangedSummarizedExperiment` objects using `recount3::create_rse()` for only a subset of samples in a particular SRA...

schelhorn

As a note to myself, in our meeting with @ChristopherWilks and @Nick-Eagles today, the idea of using a text file like the `homes_index` at https://github.com/LieberInstitute/recount3/blob/master/R/project_homes.R#L44 but for the annotation options...

lcolladotor

annotation version / genome

1

Currently, `seqinfo` is empty. It should be populated based on the genome we use. Is there a way to store the annotation (ie. gencode) inside the object? Not sure how,...

kasperdanielhansen

database disk image is malformed

1

Please ask questions about how to use `recount3` on the [Bioconductor Support Site](https://support.bioconductor.org) using the appropriate tag(s) including the one for this package. **Note**. Update the issue title to concisely...

EperLuo