ay-lab/mustache

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

Language: Python - Size: 8.76 MB - Last synced at: about 4 hours ago - Pushed at: 8 months ago - Stars: 76 - Forks: 12

ay-lab/fithic

Fit-Hi-C is a tool for assigning statistical confidence estimates to chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.

Language: Python - Size: 51.8 MB - Last synced at: about 4 hours ago - Pushed at: about 3 years ago - Stars: 89 - Forks: 19

ay-lab/dcHiC

dcHiC: Differential compartment analysis for Hi-C datasets

Language: R - Size: 155 MB - Last synced at: about 4 hours ago - Pushed at: over 1 year ago - Stars: 72 - Forks: 11

ay-lab/FitHiChIP

Statistically Significant loops from HiChIP data

Language: R - Size: 202 MB - Last synced at: about 4 hours ago - Pushed at: over 1 year ago - Stars: 44 - Forks: 20

ay-lab/SignifRT

A Quantitative Framework for the Assessment of RT Changes upon CRISPR-mediated Dissection, from Turner and Hinojosa-Gonzalez et al. (2025))

Language: R - Size: 17.6 KB - Last synced at: about 4 hours ago - Pushed at: 3 months ago - Stars: 0 - Forks: 0

ay-lab/Utilities

Various utility scripts for 3C data analysis

Language: R - Size: 436 KB - Last synced at: about 4 hours ago - Pushed at: about 3 years ago - Stars: 3 - Forks: 0

ay-lab/ExTraMapper

ExTraMapper is a tool to find Exon and Transcript-level Mappings of a given pair of orthologous genes between two organisms using sequence conservation.

Language: Python - Size: 80.6 MB - Last synced at: about 4 hours ago - Pushed at: over 3 years ago - Stars: 11 - Forks: 7

ay-lab/BGGN239Spring2025

Language: HTML - Size: 54.1 MB - Last synced at: about 4 hours ago - Pushed at: 4 months ago - Stars: 0 - Forks: 1

ay-lab/ATACProc

ATAC-seq processing pipeline

Language: Shell - Size: 138 KB - Last synced at: about 4 hours ago - Pushed at: over 3 years ago - Stars: 33 - Forks: 11

ay-lab/3D-IKAROS

Utility scripts related to IKAROS manuscript

Language: R - Size: 25.5 MB - Last synced at: about 4 hours ago - Pushed at: almost 2 years ago - Stars: 4 - Forks: 0

ay-lab/IQTL

Interaction QTL (IQTL) using HiChIP contacts

Language: R - Size: 448 KB - Last synced at: about 4 hours ago - Pushed at: 12 months ago - Stars: 7 - Forks: 1

ay-lab/Soffritto

Language: Jupyter Notebook - Size: 48.8 MB - Last synced at: about 4 hours ago - Pushed at: 6 months ago - Stars: 2 - Forks: 0

ay-lab/Colocalization

Co-localization analysis between reference GWAS and eQTL summary statistics

Language: R - Size: 97.7 KB - Last synced at: about 4 hours ago - Pushed at: over 2 years ago - Stars: 8 - Forks: 4

ay-lab/S_LDSC_SNP

Stratified LD score regression analysis

Language: Shell - Size: 30.3 KB - Last synced at: about 4 hours ago - Pushed at: over 2 years ago - Stars: 6 - Forks: 1

ay-lab/FineMap

Language: R - Size: 53.7 KB - Last synced at: about 4 hours ago - Pushed at: over 2 years ago - Stars: 3 - Forks: 5

ay-lab/ChIPLine

ChIP-seq analysis pipeline

Language: Shell - Size: 93.8 KB - Last synced at: about 4 hours ago - Pushed at: about 1 year ago - Stars: 9 - Forks: 6

ay-lab/dcHiCviz

Visualization for dcHiC files.

Size: 34.9 MB - Last synced at: about 4 hours ago - Pushed at: over 4 years ago - Stars: 2 - Forks: 0

ay-lab/GhmCN

Graphical 5hmC Convolutional Networks

Language: Python - Size: 3.2 MB - Last synced at: 5 days ago - Pushed at: over 1 year ago - Stars: 2 - Forks: 0

ay-lab/HiCnv

HiCnv is used to call copy number variations and breakpoints from Hi-C data

Language: Python - Size: 197 MB - Last synced at: about 4 hours ago - Pushed at: over 1 year ago - Stars: 21 - Forks: 5

ay-lab/HiCtrans

HiCtrans is a pipeline to call translocations from Hi-C data

Language: R - Size: 30.4 MB - Last synced at: about 4 hours ago - Pushed at: almost 4 years ago - Stars: 15 - Forks: 5

ay-lab/HiCKRy

HiCKRy is a tool developed by the Ay Lab to normalize HiC data using the Knight-Ruiz algorithm for matrix normalization.

Language: Python - Size: 16.6 KB - Last synced at: about 4 hours ago - Pushed at: about 8 years ago - Stars: 1 - Forks: 2

ay-lab/AveSim

AveSim is a pipeline to simulate Hi-C matrices involving CNVs and translocations.

Language: Perl - Size: 11.6 MB - Last synced at: about 4 hours ago - Pushed at: almost 6 years ago - Stars: 5 - Forks: 1

ay-lab/Brd2_analysis

Analysis and data from report titled 'Brd2 is dispensable for genome compartmentalization and replication timing'

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ay-lab/pieQTL_NG

Language: R - Size: 37.1 KB - Last synced at: about 4 hours ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 1

ay-lab/selfish

SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.

Language: Python - Size: 625 KB - Last synced at: about 4 hours ago - Pushed at: over 2 years ago - Stars: 17 - Forks: 7

ay-lab/BGGN239Spring2023

Language: HTML - Size: 23.4 MB - Last synced at: about 4 hours ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

ay-lab/Converters Fork of zhaoshuoxp/Converters

Format Converters: bam2bigwig, FitHiC2bigInteract/longRange, HiCPro2JuiceBox, bedGrapgh2bigwig; GTF/BAM deduplicates; dropbox link converter

Size: 23.4 KB - Last synced at: about 4 hours ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

ay-lab/bggn239

Size: 0 Bytes - Last synced at: about 4 hours ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

ay-lab/MISO Fork of yarden/MISO

MISO: Mixture of Isoforms model for RNA-Seq isoform quantitation

Size: 24.8 MB - Last synced at: about 4 hours ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

ay-lab/SLDP

Signed LD profile regression

Size: 9.77 KB - Last synced at: about 4 hours ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

ay-lab/copykat Fork of navinlabcode/copykat

Size: 21.7 MB - Last synced at: about 4 hours ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

ay-lab/tools Fork of niemasd/tools

A collection of command-line tools I wrote to make various repetitive tasks more convenient

Size: 137 KB - Last synced at: about 4 hours ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

ay-lab/DropletUtils Fork of MarioniLab/DropletUtils

Clone of the Bioconductor repository for the DropletUtils package.

Size: 537 KB - Last synced at: about 4 hours ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

ay-lab/SLE-mWGCNA Fork of bharatpanwar/SLE-mWGCNA

Multi-cell type gene co-expression network analysis reveals coordinated interferon response and cross cell-type correlations in SLE

Size: 41.4 MB - Last synced at: about 4 hours ago - Pushed at: almost 5 years ago - Stars: 3 - Forks: 1

ay-lab/FREEC Fork of BoevaLab/FREEC

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data

Size: 58.1 MB - Last synced at: about 4 hours ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

ay-lab/karyoploteR Fork of bernatgel/karyoploteR

karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome

Size: 2.14 MB - Last synced at: about 4 hours ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

ay-lab/gggenomes Fork of thackl/gggenomes

A grammar of graphics for comparative genomics

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ay-lab/about-dcHiC Fork of jeffreygwang/about-dcHiC

A short run-down of dcHiC (my research project)

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ay-lab/CITE-count Fork of ndu-bioinfo/CITE-count

Read and QC totalseq A fastq files and export count ADT matrix, merge with sc RNASeq data and export to scanpy

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ay-lab/RNA_SEQ_PIPELINE Fork of ndu-bioinfo/RNA_SEQ_PIPELINE

RNA-seq data processing and QC

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ay-lab/delly Fork of dellytools/delly

DELLY2: Structural variant discovery by integrated paired-end and split-read analysis

Size: 33.8 MB - Last synced at: about 4 hours ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

ay-lab/klib Fork of attractivechaos/klib

A standalone and lightweight C library

Size: 1.19 MB - Last synced at: about 4 hours ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

ay-lab/mio Fork of vimpunk/mio

Cross-platform C++11 header-only library for memory mapped file IO

Size: 193 KB - Last synced at: about 4 hours ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

ay-lab/sra-explorer Fork of ewels/sra-explorer

Web application to explore the Sequence Read Archive.

Size: 310 KB - Last synced at: about 4 hours ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

ay-lab/straw Fork of moshe-olshansky/straw

Extract data quickly from Juicebox via straw

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ay-lab/cooler Fork of open2c/cooler

A cool place to store your Hi-C

Size: 87.9 MB - Last synced at: about 4 hours ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

ay-lab/PyTorch-VAE Fork of AntixK/PyTorch-VAE

A Collection of Variational Autoencoders (VAE) in PyTorch.

Size: 45.4 MB - Last synced at: about 4 hours ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

ay-lab/LJI_RNA_SEQ_PIPELINE_V2 Fork of ndu-bioinfo/LJI_RNA_SEQ_PIPELINE_V2

Snakemake based RNA-Seq QC pipeline for cloud/cluster implementation

Size: 2.71 MB - Last synced at: about 4 hours ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

ay-lab/SIP Fork of PouletAxel/SIP

SIP: Significant Interaction Peak caller

Size: 862 KB - Last synced at: about 4 hours ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

ay-lab/LJI_RNA_SEQ_QC_PIPELINE_V1

Language: Python - Size: 7.66 MB - Last synced at: about 4 hours ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

ay-lab/chromosight Fork of koszullab/chromosight

Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps

Size: 21.2 MB - Last synced at: about 4 hours ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 1

ay-lab/HiC-Pro Fork of nservant/HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing

Language: Python - Size: 45.9 MB - Last synced at: about 4 hours ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 1

ay-lab/FitHiC-1 Fork of aryakaul/FitHiC-R

Language: R - Size: 26 MB - Last synced at: about 4 hours ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

ay-lab/igv Fork of igvteam/igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

Language: Java - Size: 374 MB - Last synced at: about 4 hours ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

ay-lab/EAST Fork of ucrbioinfo/EAST

EAST: Efficient and Accurate Detection of Topologically Associating Domains from Contact Maps

Language: Python - Size: 40 KB - Last synced at: about 4 hours ago - Pushed at: almost 8 years ago - Stars: 0 - Forks: 0

ay-lab/gatk Fork of broadgsa/gatk

Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository

Language: Java - Size: 596 MB - Last synced at: about 4 hours ago - Pushed at: about 8 years ago - Stars: 0 - Forks: 0