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1kg_ld_utils

utils/notes for LD calculation from 1000 genomes panel

3dchromatin_replicateqc

Software to compute reproducibility and quality scores for Hi-C data

abstention

Algorithms for abstention, calibration and domain adaptation to label shift.

affinity_distillation

alzheimers_parkinsons

Collaboration with Montine, Chang, and Montgomery labs on Alzheimers / Parkinson's ATAC-seq analysis

anna_pipeline_wrappers

anna_utils

mini-projects and utility functions that are useful across an array of projects that I am working on

anvil-variant-scoring

apricot

apricot implements submodular optimization for the purpose of selecting subsets of massive data sets to train machine learning models quickly.

atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline

atacseq-dnaseseq-chrombpnet-modelzoo-pipeline

ataqc

atlas_resources

A nucleotide-resolution, context-specific sequence annotation of the dynamic regulatory landscape of the human and mouse genomes

av_scripts

A place to track my scripts with git.

avutils

Place to start factoring out code from av scripts

basepairmodels

bcl2fastq-docker

bcolz

A columnar data container that can be compressed.

bds_pipeline_modules

BigDataScript (BDS) pipelines and modules

bias_correction

Bias correction -- GC and enzymatic bias

bpnet

Toolkit to train base-resolution deep neural networks on functional genomics data and to interpret them

bpnet-manuscript

BPNet manuscript code.

bpnet-refactor

bulk-rna-seq

Pipeline for gecco RNA-seq analysis

cardiogenesis_repo

Cardiogenesis Repo

char-rnn

Multi-layer Recurrent Neural Networks (LSTM, GRU, RNN) for character-level language models in Torch

chip-nexus-pipeline

ChIP-nexus pipeline

chip-seq-pipeline2

ENCODE ChIP-seq pipeline

chipseq_dip_finder

Identifies the location of a histone binding site from histone chip-seq narrowPeak calls.

chipseqvnewtech

Place to store code relevant to Jamboree