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Mild atopic dermatitis is characterized by increase in non-staphylococcus pathobionts and loss of specific species – Lize Delanghe – Scientific Reports
https://www.nature.com/articles/s41598-024-74…
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I'm analyzing a transcript (TCONS_00028547) that's differentially expressed between two conditions. I've noticed that the TPM values that appear in sleuth live are different from the ones I get from s…
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Updating implementation of `differential_abundance.datasets.utils._simulate_treatment` to generate condition labels with IWD approach. Should include:
- Picking minima/maxima with geosketching on P…
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First, thanks for developing and maintaining this amazing tool!
I got warnings while running `ancombc2` with the following command. These happened with my dataset, but not with the example datasets…
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Hi again,
first of all, this package is amazing!
I'm dealing with heat_tree_matrix on data obtained with calc_diff_abund_deseq2; what should I do on the diff_table in order to
keep in considerat…
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Write data loader function to:
1. Take anndata object as input
2. Run `_simulate_treatment` multiple times varying parameters
3. Store simulated condition labels as columns in `obs` with `*_seed…
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Hi,
After running the merge step,
/stringtie-1.3.3b/stringtie -eB -p 8 -G stringtie_merged.gtf -A abundance/S${i}.gene_abundance.tab -o ballgown/S${i}/S${i}.genome.gtf ${i}.mapped.sorted.bam
…
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The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival – Philipp Licht – NPJ Biofilms Microbiomes
https://www.nature.com/articles/s41522-024-00542-4
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Sustained gut dysbiosis and intestinal inflammation show correlation with weight gain in person with chronic HIV infection on antiretroviral therapy - Aya Ishizaka – BMC Microbiology
https://bmcmic…
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Hi,
I am just started to work with metacoder, but I have a simple question. When I import a phyloseq object with parse phyloseq I can see the all components correctly imported. However, in the otu_t…