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Hi,
This is my first time using SPEAQeasy and I have the following error:
```
Error executing process > 'PullTranscriptFasta (Downloading TX FA File: gencode.v40.transcripts.fa)'
Caused by:…
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It seems that the option `--force_strand` mentioned twice in http://research.libd.org/SPEAQeasy/pipeline-overview.html has been removed recently (or never implemented?). I suppose that `--strand_mode …
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When using the `--strand_mode "declare"` option, a user can treat all samples as a particular strandness pattern, regardless of what SPEAQeasy infers about strandness. However, it's currently difficul…
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While we actually perform transcript quantification (via Kallisto/Salmon) for rat, we never construct the final `SummarizedExperiment` object `rse_tx`. A couple pieces are missing: a `feature_to_Tx*.r…
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### Description of the bug
Hi, I ran circdna pipeline on bam files using identifier circle_finder, it broken with exit status 140 while `executing process > 'NFCORE_CIRCDNA:CIRCDNA:SAMTOOLS_SORT_QNAM…
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The idea is to update the file structure to reflect https://lcolladotor.github.io/bioc_team_ds/organizing-your-work.html#jhpce-file-organization.
## `Roche_Habenula`
- [x] `habenula_*csv` -> `ra…
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Unlike #1 and #2 where we'll explore how some sample covariates are related to the gene expression, here we'll explore how the covariates are related to each other.
We have some study design covari…
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Explore whether we can use the example data from `tximport` to create an RSE from `Salmon` transcript count output files and run the qSVA functions on it.
See:
* http://bioconductor.org/packages…
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Gene enrichment was calculated as part of spatial registration analysis. Pick the top 3-5 genes (use getTopN() from spatial registration git issue) from each cluster based on the t-statistic. Plot the…
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For each `k` from our `BayesSpace` results, can you create a heatmap of let's say the top 10 marker genes for each DLPFC layer?
To do so, you can load the marker genes with (or `read.csv()` from b…