ajlee21 Goto Github PK

adage

This is the repository for ADAGE (Analysis using Denoising Autoencoders for Gene Expression)

ajlee21.github.io

Personal website for Alexandra Lee

biobombe

BioBombe: Sequentially compressed gene expression features enhances biological signatures

cmappy

Assorted tools for interacting with .gct, .gctx files and other Connectivity Map (Broad Institute) data/tools

common-microbes

Identifying commonly found microbes

core-accessory-interactome

Investigating the functional relationship between P. aeruginosa core and accessory genes.

covid19-review

A collaborative review of the emerging literature on diagnostics and treatments related to COVID-19

cyclegan_gene_expression

Experimenting using cycleGAN to transform P. aeruginosa gene expression data between planktonic and biofilm conditions.

danich1.github.io

Personal webiste for David Nicholson

deep-review

A collaboratively written review paper on deep learning, genomics, and precision medicine

deep-rules

Ten Quick Tips for Deep Learning in Biology

deprior

generic-expression-patterns

Distinguishing between generic and experiment-specific gene expression signals.

greenelab.com

The website source code for greenelab.com

intro-to-svgs

Presentation and reference on the basics of SVGs, for academics

iscb-diversity-manuscript

Analysis of ISCB Fellows and Keynotes Reveals Disparities

jupyter-intro-xfel-jan17

Introduction to Jupyter Notebook

knowledge-graph-review

A literature review for constructing and using knowledge graphs in a biomedical setting.

lincs_latent_space

Training VAE on LINCS dataset.

onboarding

Onboarding materials for the Greene Lab

pa-seq-compendia

To build compendia of publicly available RNAseq data for P. aeruginosa, specifically.

pancancer

Building classifiers using cancer transcriptomes across 33 different cancer-types

ponyo

Software to simulate compendium-wide gene expression data using a VAE.

pseudomonas_latent_spaces

To explore the use of latent space transformations using pseudomonas transcriptomic data.

python_bootcamp

Course materials for 4 week python programming bootcamp at Penn

python_bootcamp_2020

simulate-expression-compendia

Evaluating the effect of technical sources of variability in large-scale gene expression compendia.

snorkeling

Extracting biomedical relationships from literature with Snorkel 🏊

sophie

Software to distinguish between common and experiment-specific gene expression signals

t2d_prediction

Predict T2D associated loci