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Large-scale Benchmarking of Microbial Multivariable Association Methods

License: MIT License

R 100.00%
microbiome benchmarking differential-abundance-analysis differential-abundance-methods metagenomics synthetic-dataset-generation biobakery multiple-covariates repeated-measures false-discovery-rate

benchmarkmicrobiome's Introduction

Hello, World!

Himel is a tenure-track Principal Investigator researching at Cornell University's Department of Population Health Sciences. Himel is also an Adjunct Faculty of Statistics and Data Science at Cornell. He develops computational methods to generate and validate testable hypotheses that accelerate data-driven discovery. Prior to Cornell, Himel was an Associate Principal Scientist (Associate Director) at Merck Research Laboratories and a postdoctoral fellow of Computational Biology and Bioinformatics at Harvard University.

Himel holds a Bachelor of Science (B.Sc.) degree in Statistics from the University of Calcutta and a Master of Science (M.Sc.) degree in Statistics from the Indian Institute of Technology (IIT) Kanpur. He earned his Ph.D. in Biostatistics from the University of Alabama at Birmingham (UAB).

As background, Himel is a Julia enthusiast, a Python explorer, and an R developer. Mostly, he develops computational methods and open-source software for the analysis of high-dimensional omics and imaging modalities with a particular emphasis on spatial, temporal, and spatiotemporal multimodal data. Himel is also an extended lab member of the bioBakery software development team at the Harvard Chan School and the Broad Institute.

A recipient of the 2022 IISA Early Career Award in Statistics and Data Sciences, Himel is a Fellow of the American Statistical Association (FASA) and an Elected Member of the International Statistical Institute.

For more information, please visit his website at himelmallick.org and feel free to get in touch on Twitter or on LinkedIn.

โœ Blog & Writing

I am an occasional blog writer and you can find my blog articles on my website at himelmallick.org. I am also engaged in publishing papers in peer-reviewed journals. A complete list of my publications can be found on Google Scholar.

๐Ÿ“ˆ GitHub Stats

Himel's github stats

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benchmarkmicrobiome's Issues

Error in names(simlist) <- simnames

Very cool project!

I had to remove the forward slash in '/Library/sparseDOSSAhelperFunctions.R' from line 106 of the file Load_Simulator.R to remove the error:

Error in file(filename, "r", encoding = encoding) :
  cannot open the connection
Calls: <Anonymous> -> sourceURL -> source -> file
In addition: Warning message:
In file(filename, "r", encoding = encoding) :
  cannot open file '/Library/sparseDOSSAhelperFunctions.R': No such file or directory
Execution halted 

However I get the following error after running the code:
Rscript Codes/Load_Simulator.R --metadataType UVB --nSubjects 5 --nPerSubject 1 --nMicrobes 10 --spikeMicrobes 0.1 --nMetadata 1 --spikeMetadata 1 --effectSize 20 --workingDirectory ~/BenchmarkMicrobiome/

Error in names(simlist) <- simnames :
  'names' attribute [100] must be the same length as the vector [78]
Calls: trigger_sparseDOSSA_Simulator
Execution halted

Enhancesments

  • The eval_res_list_repeated function should not return factor values for the numeric entries
  • Add a few new methods previously included mgS2, limma2, ZIBBSeq, etc.
  • Add a sophisticated summary function per (q, alpha) combination
  • Revisit normalizations so that they do not output normalized values (except for TSS, RFA, and CLR)
  • Wrap the functionalities into a more streamlined R package

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