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2021_viraltissueworkshop

adamklie.github.io

agp_exercise_analysis

Analysis of existing American Gut Project data on exercise frequency

atac_v1_e18_brain_fresh_5k

awesome-cellular-programs

Community-curated list of software packages and data resources for identifying cellular programs in genomics data

awesome-grn-inference

Community-curated list of software packages and data resources for inferring gene regulatory networks (GRNs) from genomics data

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

beng182project

BENG 182 Protein Database Query Project

bimm185project

Microbial Profile Generation

bobs_toolbelt

A Python toolkit for bioinformatic research

bpnet-lite

This repository hosts a minimal version of a Python API for BPNet.

cagi6-prs-docker

Dockerized builds for CAGI6-PRS challenge

carter-lab-site

cellcommander

Common single cell analysis tasks made runnable with the command line

chen2019_cell-line-mixture_snare-seq

SNARE-seq on mixtures of cultured human BJ, H1, K562 and GM12878 cells and collected 1,047 paired profiles

crispr-jamboree

2nd IGVF CRISPR-JAMBOREE

cse253_pa1

PA1 Logistic and Softmax Regression

cse253_pa4

PA4 Image Captioning

dragonnfruit

A method for analyzing scATAC-seq experiments.

drpredict

Drug Response Predictor of Immune Checkpoint Therapy

enc4_mouse

Scripts to import ENCODE processed data for snRNA-seq experiments and snATAC-seq experiments to Seurat and ArchR objects, respectively.

encode_examples

A set of processed datasets downloaded from ENCODE for training models

eugene

Elucidating the Utility of Genomic Elements with Neural Nets

exrna_breast_cancer

Analysis of microbial sequences in exRNA for cancer prediction

fungal_endophthalmitis

Code repository for regular expression pipeline to analyze fungal endophthalmitis cases in MIMIC database

gene_program_evaluation

Evaluation framework for gene program inferred from single-cell omics data

hangauer2017_bt474_rna-seq

Repository showcasing a basic RNA-seq analysis using data from Hangauer et al 2017

neurips2021_small

paul15

Myeloid and erythroid differentiation for data of Paul et al. (2015).

predictmee

Predicting missing metadata with recurrent neural network (RNNs) based entity extraction