Phlya/adjustText
A small library for automatical adjustment of text position in matplotlib plots to minimize overlaps.
Molecular and computational biologist 3D genomics
Repositories
Phlya/tagmap
Map insertions of transopable elements using tagmentation
Phlya/pairtools_parquet
Transform 3D contacts (.pairs) to parquet
Phlya/coolpuppy_paper
Code and data used to replicate the analysis in the coolpup.py paper
Phlya/viewtools
Tools for genomic views
Phlya/hmm_bigwigs
using hmm on bigwigs
Phlya/distill-reorder-C
snakemake workflow to analyze Hi-C-like data for multiple versions of the reference genome
Phlya/biopython
Official git repository for Biopython (converted from CVS)
Phlya/hictk
Blazing fast toolkit to work with .hic and .cool files
Phlya/CoolBox
Jupyter notebook based genomic data visualization toolkit.
Phlya/resgen-python
Phlya/C-integration-mapping
[wip] mapping integration sites of defined sequences using Hi-C-like data
Phlya/Hi-CSGE
[DEPRECATED} A pipeline fastq->heatmaps for an SGE cluster based on hiclib
Phlya/bioconda-recipes
Conda recipes for the bioconda channel.
Phlya/snakemake-wrappers
This is the development home of the Snakemake wrapper repository, see
Phlya/multiprocessing-logging-feedstock
A conda-smithy repository for multiprocessing-logging.
Phlya/cooltools
The tools for your .cool's
Phlya/mustache
Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation
Phlya/pysradb
Package for fetching metadata and downloading data from SRA/ENA
Phlya/cooler
A cool place to store your Hi-C
Phlya/snakemake-qsub
Simple snakemake profile for qsub cluster
Phlya/hicplotlib
Phlya/C-TALE-Normalization
Code and examples for C-TALE normalization
Phlya/liftOverBedpe
A liftOver wrapper to accomodate BEDPE files
Phlya/higlass
Fast large scale matrix visualization for the web.
Phlya/pyGenomeTracks
python module to plot beautiful and highly customizable genome browser tracks
Phlya/selfish
SELFISH is a tool for finding differential chromatin interactions between two Hi-C contact maps.
Phlya/higlass-python
Python bindings to and Jupyter Notebook+Lab integration for the HiGlass viewer
Phlya/manual_Bonev
Finishing distiller processing of Bonev's data manually to avoid re-doing filtering
Phlya/peaktools
tools for BEDPE-style peaks