Adam Klie's Projects
Analysis of existing American Gut Project data on exercise frequency
Community-curated list of software packages and data resources for identifying cellular programs in genomics data
Community-curated list of software packages and data resources for inferring gene regulatory networks (GRNs) from genomics data
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
BENG 182 Protein Database Query Project
Microbial Profile Generation
A Python toolkit for bioinformatic research
This repository hosts a minimal version of a Python API for BPNet.
Dockerized builds for CAGI6-PRS challenge
Common single cell analysis tasks made runnable with the command line
SNARE-seq on mixtures of cultured human BJ, H1, K562 and GM12878 cells and collected 1,047 paired profiles
2nd IGVF CRISPR-JAMBOREE
PA1 Logistic and Softmax Regression
PA4 Image Captioning
A method for analyzing scATAC-seq experiments.
Drug Response Predictor of Immune Checkpoint Therapy
Scripts to import ENCODE processed data for snRNA-seq experiments and snATAC-seq experiments to Seurat and ArchR objects, respectively.
A set of processed datasets downloaded from ENCODE for training models
Elucidating the Utility of Genomic Elements with Neural Nets
Analysis of microbial sequences in exRNA for cancer prediction
Code repository for regular expression pipeline to analyze fungal endophthalmitis cases in MIMIC database
Evaluation framework for gene program inferred from single-cell omics data
Repository showcasing a basic RNA-seq analysis using data from Hangauer et al 2017
Myeloid and erythroid differentiation for data of Paul et al. (2015).
Predicting missing metadata with recurrent neural network (RNNs) based entity extraction