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Hi @EricKutschera
When I ran ESPRESSO, the abundance file reported around 13,000 genes, but rmats-long produced a `differential_genes.tsv` file with only 9,800 genes. I'm a bit confused about how …
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Hi, thanks to @henry2cox 's help in: https://github.com/linux-test-project/lcov/issues/314, I managed to get something a lot better running ... But after a couple of days of data collection, I am seei…
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For key stats explore if magnitude, proportion or percentile rank is more differential
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Hi there,
Just a query regarding the functionality of FindNhoodGroupMarkers and testDiffExp.
My understanding is that when we group together neighborhoods using groupNhoods the aggregated outp…
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[simulate_data.txt](https://github.com/dieterich-lab/riboseq-utils/files/1457261/simulate_data.txt)
TE can be estimated using a simulation approach based on modifying real data to introduce diffe…
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Hello @EricKutschera,
is there a way to do this `classify_isoform_differences.py` for all isoforms? not doing individually for each isoform so that I have at the end all isoform in a single tsv fi…
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I read through the paper and went through the tutorial and I am having trouble figuring out how to best use the outputs. From the outputs is it possible to get cell type specific counts for each gene …
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### Description of the bug
Hello, I am a co-worker of olgabot and this issue is following [issue 196](https://github.com/nf-core/differentialabundance/issues/196). Running the nf-core/differentialabu…
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tRNAs and mitochondrial RNAs can make up a large proportion of mapped reads and thus bias the normalization and differential gene expression procedure.
For example: "tRNA genes and genes covered b…
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I am running make_hicexp() on my data for 14 chromosomes. My spares matrices seem to be fine for each chromosome. Somehow the hicexp@hic_table is empty for last two chromosomes, but it doesn't give me…