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3d-ikaros

Utility scripts related to IKAROS manuscript

about-dchic

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

atacproc

ATAC-seq processing pipeline

avesim

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

bggn213_w23

Winter 2023 BGGN-213 class website

bggn239

bggn239spring2023

brd2_analysis

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

chipline

ChIP-seq analysis pipeline

chromosight

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

cite-count

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

colocalization

Co-localization analysis between reference GWAS and eQTL summary statistics

conditional_eqtl

converters

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

cooler

A cool place to store your Hi-C

copykat

dchic

dcHiC: Differential compartment analysis for Hi-C datasets

dchicviz

Visualization for dcHiC files.

delly

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

dropletutils

Clone of the Bioconductor repository for the DropletUtils package.

east

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

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.

finemap

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.

fithic-1

fithichip

Statistically Significant loops from HiChIP data

freec

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

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

gggenomes

A grammar of graphics for comparative genomics

ghmcn

Graphical 5hmC Convolutional Networks