1st lesson free
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Shah
- Rate $35
- Response 1h
-
Students3
Number of students Shah has accompanied since arriving at Superprof
Number of students Shah has accompanied since arriving at Superprof
$35/h
Contact
1st lesson free
- Statistics
- SVT
- Biochemistry
- Exam Prep- Sciences BAC
Metagenomics & microbiome data analysis — MetaPhlAn, HUMAnN, LEfSe, taught by a PhD researcher
- Statistics
- SVT
- Biochemistry
- Exam Prep- Sciences BAC
Lesson location
About Shah
I'm a PhD researcher at SEMM working under Prof. Nicola Segata, whose group develops MetaPhlAn, HUMAnN, ChocoPhlAn and LEfSe — the standard toolkit for shotgun metagenomic profiling. I use these tools daily on real data, not from documentation.
My work covers taxonomic and functional profiling, strain-level analysis, and machine learning applied to microbiome datasets. I've also taught biology for 7 years, so I can explain why a method works, not just which command to type.
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About the lesson
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- English
All languages in which the lesson is available :
English
Metagenomics has a steep entry cost: the biology, the command line, and the statistics all have to click at once. I teach them together, using real data.
From sample to results — study design, 16S vs shotgun (and when each is the wrong choice), read QC, host decontamination, and what your sequencing depth actually supports.
Taxonomic and functional profiling — MetaPhlAn and HUMAnN end to end: running them, reading the output tables, and interpreting what a relative abundance profile does and doesn't tell you. Strain-level analysis and assembly-based approaches for those who need them.
Statistics and interpretation — alpha and beta diversity, compositional data and why standard methods mislead on it, differential abundance with LEfSe and alternatives, and multivariate testing. This is where most microbiome papers go wrong, so I spend real time here.
Machine learning on microbiome data — feature selection, cross-validation done correctly, and avoiding the overfitting that is endemic in this literature.
Your own dataset — bring your samples, your failing pipeline, or your thesis chapter. I'm happy to work through your actual analysis rather than a tutorial dataset.
For PhD and master's students, postdocs, and wet-lab researchers moving into computational microbiome work. Comfort with the command line helps but isn't required — we can start from bash basics. Online, in English, first lesson free to scope out what you need.
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Rates
Rate
- $35
Pack rates
- 5 h: $175
- 10 h: $350
free lessons
This first lesson offered with Shah will allow you to get to know each other and clearly specify your needs for your next lessons.
- 1hrs
online
- $35/h
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