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DON'T submit
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It seems like a bug that `sig_transcripts` at https://github.com/LieberInstitute/qsvaR/blob/498143f803362e76dfca87ac81cee354a5c29416/R/qSVA.R#L23 is not used later on the `qSVA()` function.
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[24.08.2023 12:08:06] jasiu-rozowyczlowiek:
[24.08.2023 12:08:06] jasiu-rozowyczlowiek
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[24.08.2023 12:08:18] jasiu-rozowyczlowiek:
[24.08.2023 12:08:18] jasiu-rozowyczlowiek
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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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internal/metamorphic/crossversion/crossversion_test.TestMetaCrossVersion [failed](https://buildConfiguration/Cockroach_Nightlies_NightlyPebbleMetamorphicCrossversion/7593487?buildTab=log) with [artifa…
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adding DESeq models with interactions to pipeline
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Because the region_matrix.py code (which is very old) doesn't work in Python 3.
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```
xinhe@sidbdri:~/Projects/snakemake_single$ ls -l results/final_bams/
total 4172
lrwxrwxrwx 1 xinhe xinhe 26 Feb 1 02:20 1467_A.rat.bam -> ../mapped_reads/1467_A.bam
-rw-rw-r-- 1 xinhe xi…
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It's always nice to impose some kind of ordering on the samples so that, e.g., the FPKM columns in the output spreadsheets are grouped together in some rational way (for example, all WT samples togeth…