• Stars
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    31
  • Rank 819,886 (Top 17 %)
  • Language
    Python
  • License
    BSD 3-Clause "New...
  • Created almost 8 years ago
  • Updated about 4 years ago

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Repository Details

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1

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dragonn

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3

atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline
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4

bpnet

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5

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6

chrombpnet

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7

chipseq_pipeline

AQUAS TF and histone ChIP-seq pipeline
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8

dfim

Deep Feature Interaction Maps (DFIM)
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9

phantompeakqualtools

This package computes informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.
R
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10

ChromDragoNN

Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts"
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11

3DChromatin_ReplicateQC

Software to compute reproducibility and quality scores for Hi-C data
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12

alzheimers_parkinsons

Collaboration with Montine, Chang, and Montgomery labs on Alzheimers / Parkinson's ATAC-seq analysis
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43
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13

genomelake

Simple and efficient access to genomic data for deep learning models.
Python
43
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14

simdna

A python library for creating simulated regulatory DNA sequences
Python
38
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15

abstention

Algorithms for abstention, calibration and domain adaptation to label shift.
Python
36
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16

coda

Coda: a convolutional denoising algorithm for genome-wide ChIP-seq data
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17

cs273b

CS273B Deep Learning for Genomics Course Materials
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18

coessentiality

Companion to "A genome-wide almanac of co-essential modules assigns function to uncharacterized genes" (https://doi.org/10.1101/827071)
Python
27
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19

genomedisco

Software for comparing contact maps from HiC, CaptureC and other 3D genome data.
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20

training_camp

Genetics training camp
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21

gkmexplain

Accompanying repository for GkmExplain paper
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21
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22

fastISM

In-silico Saturation Mutagenesis implementation with 10x or more speedup for certain architectures.
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23

ataqc

Python
17
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24

basepairmodels

Python
16
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25

labelshiftexperiments

Label shift experiments
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26

seqdataloader

Sequence data label generation and ingestion into deep learning models
Python
12
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27

bpnet-manuscript

BPNet manuscript code.
Jupyter Notebook
11
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28

higlass-dynseq

Dynamic sequence track for HiGlass
JavaScript
11
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29

DeepBindToKeras

Convert DeepBind models to Keras
C
11
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30

ProCapNet

Repository for modeling PRO-cap data with the BPNet-like model, ProCapNet.
Jupyter Notebook
11
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31

MPRA-DragoNN

Code accompanying the paper "Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays"
Python
11
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32

mpra

Deep learning MPRAs
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9
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33

ENCODE_scatac

Python
8
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34

variant-scorer

A framework to score and analyze variant effects genome-wide using ChromBPNet models
Python
8
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35

tronn

Transcriptional Regulation (Optimized) Neural Nets (TRoNN)
Python
8
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36

Cardiogenesis_Repo

Cardiogenesis Repo
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8
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37

deepbind

I have put my modified version of the deepbind code here.
C
8
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38

scATAC-reprog

Code for the analysis performed in the paper "Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency" by Nair, Ameen et al.
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7
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39

veryolddontuse_deeplift_modisco_tutorial

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6
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40

chromovar3d

Code from the chromatin variation 3d project
JavaScript
6
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41

chip-nexus-pipeline

ChIP-nexus pipeline
Python
6
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42

kerasAC

keras accessibility models: code to train, predict, interpret
Python
6
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43

DART-Eval

Jupyter Notebook
6
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44

DMSO

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5
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45

mesoderm

Scripts for dataset processing and QC for the mesoderm differentiation project.
HTML
5
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46

1kg_ld_utils

utils/notes for LD calculation from 1000 genomes panel
Shell
5
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47

keras-genomics

Genomics layers for Keras 2
Python
5
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48

lsgkm-svr

lsgkm+gkmexplain with regression functionality. Builds off kundajelab/lsgkm (which has gkmexplain), which in turn builds off Dongwon-Lee/lsgkm (the original lsgkm repo)
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49

yuzu

yuzu is a compressed-sensing based approach for quickly calculating in-silico mutagenesis saliency.
Python
5
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50

PFBoost

modular 2D boosting code with stabilization and hierarchies
Python
4
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51

coessentiality-browser

Gene browser using coessentiality and related data
Python
4
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52

zenodo_upload

Python script to upload files to Zenodo
Python
4
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53

neural_motif_discovery

Framework for interrogating transcription-factor motifs and their syntax/grammars from neural-network interpretations
Jupyter Notebook
4
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54

vizsequence

Collecting commonly-repeated sequence visualization code here
Python
4
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55

av_scripts

A place to track my scripts with git.
Jupyter Notebook
4
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56

bpnet-refactor

Python
3
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57

dynseq-pages

3
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58

locusselect

extraction of data embeddings from deep learning model layers; computation of embedding distance and visualization with umap/tsne
Jupyter Notebook
2
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59

atlas_resources

A nucleotide-resolution, context-specific sequence annotation of the dynamic regulatory landscape of the human and mouse genomes
Shell
2
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60

tf_binding_challenge

scoring/ranking code for tf binding challenge
Python
2
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61

bulk-rna-seq

Pipeline for gecco RNA-seq analysis
Shell
2
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62

python_reading_group

Jupyter Notebook
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63

higlass-multi-tileset

Multi-tileset data fetcher for HiGlass
JavaScript
2
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64

retina-models

BPNet models for retina single-cell multiome data
Jupyter Notebook
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65

TF-Atlas

Code repository for the TF-Atlas project
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66

crispr_safe_targeting_regions

Repository for creating the CRISPR controls termed "safe harbor" regions from Morgens et al., 2017, Nat Comms.
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67

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Benchmarking interpretation methods
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68

kCCA

Python
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69

momma_dragonn

Flexible deep learning framework
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70

feature_interactions

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71

bds_pipeline_modules

BigDataScript (BDS) pipelines and modules
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72

mseqgen

Multi task batch generator for training deep learning models on CHIP-seq, CHIP-exo, CHIP-nexus, ATAC-seq, RNA-seq (or any other -seq)
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73

SVM_pipelines

Jupyter Notebook
1
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74

jamboree-toolkit

toolkit for setting up compute environment on gcp for jamborees
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75

genomics-DL-archsandlosses

A collection of Deep Learning architectures and loss functions from across the genomics literature
Python
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76

affinity_distillation

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77

SeqPriorizationCATLAS

Sequence priorization using gkm-explain.
Jupyter Notebook
1
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78

chromBPNet-tutorial

How to train BPNets on ATAC-seq data using the Basepairmodels repo from Stanford's Kundaje Lab.
Shell
1
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79

PREUSS

PREUSS: predicting RNA editing using sequence and structure
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1
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80

CTCFMutants

Jupyter Notebook
1
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