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Hi there, I'm Alex Soupir, a Postdoctoral Research Fellow at Moffitt Cancer Center šŸ‘‹

Some information for GitHub:

  • šŸ”­ Iā€™m currently working on ... growing my youtube channel teaching some bioinformatics procedures for analyzing sequencing data.
  • šŸŒ± Iā€™m currently learning ... integrating multi-omic approaches to identify causes for immunotherapy resistance.
  • šŸ‘Æ Iā€™m looking to collaborate on ... data science projects for fun - have always had a soft sport for data analysis and predictive statistics.
  • šŸ¤” Iā€™m looking for help with ... learning Python more and scripting in bash, but am really interested in learning ground up coding for software development.
  • šŸ’¬ Ask me about ... anything!
  • āš” Fun fact: ... I like teaching as much as learning. Pursuing knowledge is fun but being able to pass on knowledge is incredible too.

Languages and Tools:

R and R Studio python bash keras conda

Latest YouTube Videos

Spatial Transcriptomics - Part 4.1: Supervised Phenotyping with InSituType
Feb 6, 2024
Testing Pytorch Auto-Encoder Code (Deep Learning)
Feb 2, 2024
Spatial Transcriptomics - Part 7: Ligand-Receptor Spatial Autocorrelation
Jan 30, 2024
Docker Containers from Dockerhub with TrueNAS Scale
Jan 15, 2024
Spatial Transcriptomics - Part 6.2: Spatial Permutations of High Scores
Jan 13, 2024
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Software Packages

  • spatialTIME: R package for deriving spatial statistics from point patterns created with biological data
  • scSpatialSIM: R package for simulating biologically informed point patterns (multiplex IF, spatial transcriptomics, etc)
  • spatialGE: R package for analyzing spatial transcriptomics data informed with spatial context
  • mxfda: R package for functional data analysis of spatial statistics (no more need to pick an radius!)
  • curatedPCaData: R package of harmonized prostate cancer gene expression and copy number from almost 20 studies

Alex Soupir's Projects

cuda_conda icon cuda_conda

conda environment to interact with GPU in pytorch

endophyte icon endophyte

Package to make endophyte data processing more simple

gevisor icon gevisor

Visualization of gene expression data from GeoMx-DSP experiments

mnist_dl icon mnist_dl

Deep Learning for the Kaggle MNIST challenge

simple-genome-mining icon simple-genome-mining

Simple script to take *.fasta annotation files and compares that to a characteristic key for whether individual annotation files displayed a phenotype or not. Hypothetical proteins are removed and then the positive phenotype is compared to the negative phenotype for the difference in genome annotated genes.

snakemake icon snakemake

High throughput Next Generation Sequencing (NGS) data analysis using Python 3 Snakemake

soybean-microbiome icon soybean-microbiome

Mothur Analysis of soybean microbiome for bacterial, arbuscular mycorrhiza, and broad fungal communities.

spatialge icon spatialge

An R package for visualization and analysis of spatially-resolved gene expression

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