scottyler89
Chemistry -> bench biology -> bioinformatics -> data-scientist. NHGRI Fellow now in industry
Ideaya BiosciencesSan Francisco
Pinned Repositories
anti_correlation_vs_overdispersion
count_depth_effects
A small benchmark to look at the effects of different types of normalization determining the impact on distance measures
dclustval
A package for performing dense cluster validation
downsample
downsample columns such that the sum is equal in all columns
orthocoder
Variational Autoencoder with modified loss function, to ensure global orthogonality to input covariates
PercentMaxDiff
A metric for relative distance in Poisson sampling problems
PyMINEr
slicr
SLICR: Sparse Locally Involved Covariate Regression. A Python package for efficient, memory-conscious kNN distance correction, based on technical covariates whose effect should be removed
towcab
Topologically Overlapping Within-Cluster/Across-Batch DEGs/pathways
umap_tsne_experiment
Testing if UMAP/tSNE overfit their intrinsic dimensionality
scottyler89's Repositories
scottyler89/umap_tsne_experiment
Testing if UMAP/tSNE overfit their intrinsic dimensionality
scottyler89/PercentMaxDiff
A metric for relative distance in Poisson sampling problems
scottyler89/downsample
downsample columns such that the sum is equal in all columns
scottyler89/PyMINEr
scottyler89/dclustval
A package for performing dense cluster validation
scottyler89/orthocoder
Variational Autoencoder with modified loss function, to ensure global orthogonality to input covariates
scottyler89/towcab
Topologically Overlapping Within-Cluster/Across-Batch DEGs/pathways
scottyler89/anti_correlation_vs_overdispersion
scottyler89/count_depth_effects
A small benchmark to look at the effects of different types of normalization determining the impact on distance measures
scottyler89/slicr
SLICR: Sparse Locally Involved Covariate Regression. A Python package for efficient, memory-conscious kNN distance correction, based on technical covariates whose effect should be removed
scottyler89/dim_red_st
An interactive streamlit web-app for exploring the relatinshiop between dimension reduction & intrinsic dimensions
scottyler89/DNABERT_2
Derivative of DNABERT-2
scottyler89/ppi_diffusion
A repository beginning with a protein-protein interaction network, then diffusing a signal through it
scottyler89/saa3_cxcl10_if
IF processing and analysis for Saa3 and Cxcl10 in trained immunity experiment
scottyler89/segmented_linear_model_selection
Builds segmented linear models, selecting the best fit via BIC
scottyler89/st_rle
RLE normalization (but for python ;-)
scottyler89/story_graph
A graph network representation of stories
scottyler89/SynD_BERT
Synthetic Biology powered by a masked transformer
scottyler89/weighted_stats
an implementation of some fast weighted statistics