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For gene ranking (for GSEA, for example) and visualizations (on volcano plots, for example), DESeq author Michael Love suggests shrinking of the effect sizes (log-fold changes) with the `lfcShrink` fu…
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Hi Dr. Hou,
Thanks for your wonderful work! I am aware that Lamian is designed for multiple scRNA samples, but quite curious about whether it can handle the reduced one-sample case. In some scenari…
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Hi Mara,
I followed your video about PICRUSt2 and it was very helpful in getting my analyses done.
However, I'm still having difficulty in getting downstream statistical analysis and data visualizat…
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Hello,
I am a relatively new user of phyloseq, but it is a great program and has really helped out in our analyses. I am currently testing various methods for differential abundance analysis with o…
ghost updated
5 years ago
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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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I have run decontam on a data set that has ASV’s for tumor tissue, negative controls, and control tissue. The negative controls did not have any tissue but only reagent. The controls are non-tumor spe…
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Hi @rob-p
I have a question on the "right" way of tximport/DESeq2 after salmon quant.
Why I ask "right way" - is because I am a bit confused with the tximport vignette
1 - https://biocondu…
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Hi,
Thanks for creating this excellent package for analysing PICRUSt2 output data. I have been looking for something like this for a while now.
I have run the analysis main pipeline (ggpicrust2(…
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Hello Team,
Thank you for this package! I am working on 3 conditions which was integrated using the pearson residuals(SCTransform integratio n). These three treatments had differing cell numbers in…
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Hi,
I am struggling a little with the FPKM output of Stringtie (StringTie v1.3.5). From my understanding which is supported by your response to issue #15 (https://github.com/gpertea/stringtie/issues…