Pinned Repositories
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
CellCommander
Common single cell analysis tasks made runnable with the command line
single_cell_utilities
A set of functions and scripts for single cell data handling
EUGENe
Elucidating the Utility of Genomic Elements with Neural Nets
EUGENe_paper
Code for generating the figures and results presented in the manuscript EUGENe: A Python toolkit for sequence activity prediction and analysis
SeqData
Annotated sequence data
SeqPro
Genomic sequence preprocessing toolkit
adamklie's Repositories
adamklie/awesome-grn-inference
Community-curated list of software packages and data resources for inferring gene regulatory networks (GRNs) from genomics data
adamklie/awesome-single-cell
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
adamklie/EUGENe
Elucidating the Utility of Genomic Elements with Neural Nets
adamklie/STR_crazy
A neural network approach to eye color prediction
adamklie/bobs_toolbelt
A Python toolkit for bioinformatic research
adamklie/CellCommander
Common single cell analysis tasks made runnable with the command line
adamklie/DRPredICT
Drug Response Predictor of Immune Checkpoint Therapy
adamklie/single_cell_utilities
A set of functions and scripts for single cell data handling
adamklie/2021_viralTissueWorkshop
adamklie/adamklie.github.io
adamklie/atac_v1_E18_brain_fresh_5k
adamklie/awesome-cellular-programs
Community-curated list of software packages and data resources for identifying cellular programs in genomics data
adamklie/bpnet-lite
This repository hosts a minimal version of a Python API for BPNet.
adamklie/cagi6-prs-docker
Dockerized builds for CAGI6-PRS challenge
adamklie/carter-lab-site
adamklie/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
adamklie/CRISPR-JAMBOREE
2nd IGVF CRISPR-JAMBOREE
adamklie/dragonnfruit
A method for analyzing scATAC-seq experiments.
adamklie/enc4_mouse
Scripts to import ENCODE processed data for snRNA-seq experiments and snATAC-seq experiments to Seurat and ArchR objects, respectively.
adamklie/ENCODE_examples
A set of processed datasets downloaded from ENCODE for training models
adamklie/exRNA_breast_cancer
Analysis of microbial sequences in exRNA for cancer prediction
adamklie/gene_program_evaluation
Evaluation framework for gene program inferred from single-cell omics data
adamklie/Hangauer2017_BT474_RNA-seq
Repository showcasing a basic RNA-seq analysis using data from Hangauer et al 2017
adamklie/neurips2021_small
adamklie/paul15
Myeloid and erythroid differentiation for data of Paul et al. (2015).
adamklie/predictMEE
Predicting missing metadata with recurrent neural network (RNNs) based entity extraction
adamklie/Pytorch-VAE-tutorial
A simple tutorial of Variational AutoEncoders with Pytorch
adamklie/starter-hugo-academic
adamklie/tangermeme
Biological sequence analysis for the modern age.
adamklie/topic_grn_links
Example repo for organizing topic_grn_links project