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Current mapping functionality only maps 1:1 for sample reads:assembly, with a time-series want to reciprocally map to all samples to get differential coverage information
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### Description of the bug
Hello,
I am trying to run GSEA but I get an error when trying to process the GMT file I obtained from MSigDB.
Previously, I have executed the pipeline without the G…
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A prior dependency package for the tool exists in the MTS. But conda is also available.
Once created, consider reopening this ticket for review (add tool to http://usegalaxy.org): See: https://git…
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Activity to be done as a team with @LLansing , @glchn , @jlobri , @jonathho , @MorganCunningham , @linzhi-wu
The goal is to have a single workflow that is used by all the team and that includes th…
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For some of my projects, I find that CSS normalization decreases the variance in library size compared to raw sequencing depth. I am assuming this is one of the objectives of CSS normalization.
In …
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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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In my dataset, I have 2 conditions I would like to analyse:
- Treatment: Levels A, B and C
- Stimulation: Baseline, After Stimulation
All of the patients have a baseline measurement and a measur…
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Hello,
First, thank you for this wonderful package! I've been testing different workflows and have a question regarding peptide filtering/feature selection and how it is used for downstream normali…
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Select RNA-seq simulation: software e.g FluxSimulator, RSEM etc.
Select RNA-seq simulation: parameters.
Add to the discussion: which simulator(s) to use (1 or many) and how the simulator(s) used for…