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2017

Materials used during #NGSchool2017

avtad

Plotting average TAD heatmap for Hi-C data (give TAD segmentation and cool/hiclib interactions map).

bioconda-recipes

Conda recipes for the bioconda channel.

bioframe

Pandas utilities for tab-delimited and other genomic data files

chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline.

chromatincompartments

Compartments calling for published Hi-C datasets

connect4

Monte Carlo Tree Search Based AI Connect 4 Bot

cooltools

The tools for your .cool's

distiller-nf

A modular Hi-C mapping pipeline

dpdchrom_input_parser

fontanka

Fontanka is a set of tools to work with fountains in Hi-C data. It aims to provide a flexible Python API and specialized CLI for calling fountains from cool Hi-C files.

geoparse

Python library to access Gene Expression Omnibus Database (GEO)

gyrase_topo-seq

Exploring gyrase cleavage sites accross E. coli W3110 genome

hg

a python api for higlass

hicrep

Python implementation of HiCRep stratum-adjusted correlation coefficient of Hi-C data with Cooler sparse contact matrix support

inspectro

Hi-C spectral analysis workflow

motifssearch

In-lab cases of motifs search and manipulations

ms-advancedbiolab-skoltech

Lipidomics mass-spectrometry analysis for hometask and course project at AdvancedBioLab course at Skoltech

multiqc

Aggregate results from bioinformatics analyses across many samples into a single report.

open2c_examples

pairtools

CLI tools to process mapped Hi-C data

polychrom_workbench

pystatis

Python implementation of STATIS for analysis of several data tables

redclib

Red-C data processing

resgen-python

rklib

Rabin-Karp implementation of sequence substring search for DNA/RNA

rnadnatools

Tools for RNA-DNA data anipulation

sc_dros

tadcalling

teaching_materials