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3d-genome-processing-tutorial

A 3D genome data processing tutorial for ISMB/ECCB 2017

3dchromatin_replicateqc

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

allhic-1

ALLHiC: phasing and scaffolding polyploid genomes based on Hi-C data

artemis

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

atac-pipe

Analysis pipeline for ATAC-seq Data

bioconda-recipes

Conda recipes for the bioconda channel.

celegansatacseq

The code for Daugherty, et al 2017 - Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans

easyspeciestree

Easily construct the ML species tree with single-copy gene shared by different species

falcon-phase

FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds

genome_assembly

genomedisco

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

haenfling_et_al_2016

Data processing workflow and supplementary data for Haenfling et al. 2016 - Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods

hic-compartment

when we use Hi-c data toanalyse the chromsome compartment using homer

hic_breakfinder

hic_mapping

hic_tools

A collection of tools for Hi-C data analysis

hicnv

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

hictrans

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

in-depth-ngs-data-analysis-course

Materials for 12-day course on analyzing RNA-Seq, ChIP-Seq and variant calling data.

maker.sh

The annotation of eukaryotic genome

projectils

Interpretation of T cell states using reference single-cell atlases

rna-seq

The lsf system

rnaseq-workflow

A repository for setting up a RNAseq workflow

salsa

SALSA: A tool to scaffold long read assemblies with Hi-C data

snakemake_atac

sniffles

Structural variation caller using third generation sequencing

svaba

Structural variation and indel detection by local assembly

tutorials