Spectral decomposition for characterizing long-range interaction profiles in Hi-C maps

Related tags

Geolocationinspectral
Overview

Inspectral

Spectral decomposition for characterizing long-range interaction profiles in Hi-C maps.

Snakemake workflow for the unsupervised method presented in Spracklin, Abdennur et al., 2021.

Steps

  1. Place supplementary bigwig file information in config/track_metadata.tsv to include in graphical outputs. Must be tab-delimited, including header. Must have columns:
  • Name: a display name
  • ID: a unique identifier to use in the database (can be the same as Name)
  • FileFormat: must be the string bigWig
  • Path: a local path to the file
  1. Edit config.yaml.

  2. Run:

# Generate pre-aggregated supplementary bigwig tracks if provided
$ snakemake make_track_db --force --cores all

# Run the pipeline
$ snakemake --cores all
You might also like...
Deal with Bing Maps Tiles and Pixels / WGS 84 coordinates conversions, and generate grid Shapefiles

PyBingTiles This is a small toolkit in order to deal with Bing Tiles, used i.e. by Facebook for their Data for Good datasets. Install Clone this repos

Python library to visualize circular plasmid maps
Python library to visualize circular plasmid maps

Plasmidviewer Plasmidviewer is a Python library to visualize plasmid maps from GenBank. This library provides only the function to visualize circular

Implemented a Google Maps prototype that provides the shortest route in terms of distance

Implemented a Google Maps prototype that provides the shortest route in terms of distance, the fastest route, the route with the fewest turns, and a scenic route that avoids roads when provided a source and destination. The algorithms used were DFS, BFS, A*, and Iterative Depth First Search.

"MST++: Multi-stage Spectral-wise Transformer for Efficient Spectral Reconstruction" (CVPRW 2022) & (Winner of NTIRE 2022 Challenge on Spectral Reconstruction from RGB)

MST++: Multi-stage Spectral-wise Transformer for Efficient Spectral Reconstruction (CVPRW 2022) Yuanhao Cai, Jing Lin, Zudi Lin, Haoqian Wang, Yulun Z

Code for Blind Image Decomposition (BID) and Blind Image Decomposition network (BIDeN).
Code for Blind Image Decomposition (BID) and Blind Image Decomposition network (BIDeN).

arXiv, porject page, paper Blind Image Decomposition (BID) Blind Image Decomposition is a novel task. The task requires separating a superimposed imag

Just imagine normal bancho, but you can have multiple profiles and funorange speed up maps ranked

Local osu! server Just imagine normal bancho, but you can have multiple profiles and funorange speed up maps ranked (coming soon)! Windows Setup Insta

Create rangebased on lists or values of the range itself. Range any type. Can you imagine?

funcao-allrange-for-python3 Create rangebased on lists or values of the range itself. Range any type. Can you imagine? WARNING!!! THIS MODULE DID NOT

Range Image-based LiDAR Localization for Autonomous Vehicles Using Mesh Maps
Range Image-based LiDAR Localization for Autonomous Vehicles Using Mesh Maps

Range Image-based 3D LiDAR Localization This repo contains the code for our ICRA2021 paper: Range Image-based LiDAR Localization for Autonomous Vehicl

Example of animated maps in matplotlib + geopandas using entire time series of congressional district maps from UCLA archive. rendered, interactive version below
Example of animated maps in matplotlib + geopandas using entire time series of congressional district maps from UCLA archive. rendered, interactive version below

Example of animated maps in matplotlib + geopandas using entire time series of congressional district maps from UCLA archive. rendered, interactive version below

Clip Bing Maps backgound as RGB geotif image using center-point from vector data of a shapefile and Bing Maps zoom

Clip Bing Maps backgound as RGB geotif image using center-point from vector data of a shapefile and Bing Maps zoom. Also, rasterize shapefile vectors as corresponding label image.

Color maps for POV-Ray v3.7 from the Plasma, Inferno, Magma and Viridis color maps in Python's Matplotlib
Color maps for POV-Ray v3.7 from the Plasma, Inferno, Magma and Viridis color maps in Python's Matplotlib

POV-Ray-color-maps Color maps for POV-Ray v3.7 from the Plasma, Inferno, Magma and Viridis color maps in Python's Matplotlib. The include file Color_M

Autoformer: Decomposition Transformers with Auto-Correlation for Long-Term Series Forecasting
Autoformer: Decomposition Transformers with Auto-Correlation for Long-Term Series Forecasting

Autoformer (NeurIPS 2021) Autoformer: Decomposition Transformers with Auto-Correlation for Long-Term Series Forecasting Time series forecasting is a c

Implementation for our ICCV2021 paper: Internal Video Inpainting by Implicit Long-range Propagation
Implementation for our ICCV2021 paper: Internal Video Inpainting by Implicit Long-range Propagation

Implicit Internal Video Inpainting Implementation for our ICCV2021 paper: Internal Video Inpainting by Implicit Long-range Propagation paper | project

Multivariate Time Series Forecasting with efficient Transformers. Code for the paper
Multivariate Time Series Forecasting with efficient Transformers. Code for the paper "Long-Range Transformers for Dynamic Spatiotemporal Forecasting."

Spacetimeformer Multivariate Forecasting This repository contains the code for the paper, "Long-Range Transformers for Dynamic Spatiotemporal Forecast

Codes for "Efficient Long-Range Attention Network for Image Super-resolution"

ELAN Codes for "Efficient Long-Range Attention Network for Image Super-resolution", arxiv link. Dependencies & Installation Please refer to the follow

Synthesizing Long-Term 3D Human Motion and Interaction in 3D in CVPR2021

Long-term-Motion-in-3D-Scenes This is an implementation of the CVPR'21 paper "Synthesizing Long-Term 3D Human Motion and Interaction in 3D". Please ch

Wikidata scholarly profiles

Scholia is a python package and webapp for interaction with scholarly information in Wikidata. Webapp As a webapp, it currently runs from Wikimedia To

Wikidata scholarly profiles

Scholia is a python package and webapp for interaction with scholarly information in Wikidata. Webapp As a webapp, it currently runs from Wikimedia To

Profil3r is an OSINT tool that allows you to find potential profiles of a person on social networks, as well as their email addresses 🕵️
Profil3r is an OSINT tool that allows you to find potential profiles of a person on social networks, as well as their email addresses 🕵️

Profil3r is an OSINT tool that allows you to find potential profiles of a person on social networks, as well as their email addresses. This program also alerts you to the presence of a data leak for the found emails.

Comments
  • iterative correction bug in inspectro

    iterative correction bug in inspectro

    After installing inspectro from environment file the rule eigdecomp has failed with this error: image

    Upgrading cooltools (installed locally from GitHub) and changing the import in eigendecomposition script (from cooltools.api.eigdecomp import _filter_heatmap, _fake_cis) fixes it.

    opened by agalitsyna 1
  • Inspectro module

    Inspectro module

    Technical improvements:

    • pyproject.toml allows installing inspectro system-wide
    • instructions for installation updated
    • Snakemake runs pip-installed inspectro instead of local "utils" module

    Functionality improvement:

    • cis decomposition added (both utils and Snakemake)
    • config option to run either cis or trans eigdecomp
    • projection function added to utils module

    Small improvements:

    • Docs improvements and code structure fixes in utils
    opened by agalitsyna 0
  • Eigen Decompsition

    Eigen Decompsition

    I was trying the pipeline with HT1080 HI-C data (.mcool generated from distiller.nf). Unfortunately, eigdecomp rule never worked. I think it is the problem with partition. I am sending you my SRA code (SRR7586416, SRR7586418). Please tell me what to do.

    opened by Sen0108 16
Releases(v0.1.1)
Owner
Nezar Abdennur
Nezar Abdennur
A compilation of several single-beam bathymetry surveys of the Caribbean

Caribbean - Single-beam bathymetry This dataset is a compilation of several single-beam bathymetry surveys of the Caribbean ocean displaying a wide ra

Fatiando a Terra Datasets 0 Jan 20, 2022
A simple reverse geocoder that resolves a location to a country

Reverse Geocoder This repository holds a small web service that performs reverse geocoding to determine whether a user specified location is within th

4 Dec 25, 2021
Solving the Traveling Salesman Problem using Self-Organizing Maps

Solving the Traveling Salesman Problem using Self-Organizing Maps This repository contains an implementation of a Self Organizing Map that can be used

Diego Vicente 3.1k Dec 31, 2022
framework for large-scale SAR satellite data processing

pyroSAR A Python Framework for Large-Scale SAR Satellite Data Processing The pyroSAR package aims at providing a complete solution for the scalable or

John Truckenbrodt 389 Dec 21, 2022
Yet Another Time Series Model

Yet Another Timeseries Model (YATSM) master v0.6.x-maintenance Build Coverage Docs DOI | About Yet Another Timeseries Model (YATSM) is a Python packag

Chris Holden 60 Sep 13, 2022
Python 台灣行政區地圖 (2021)

Python 台灣行政區地圖 (2021) 以 python 讀取政府開放平台的 ShapeFile 地圖資訊。歡迎引用或是協作 另有縣市資訊、村里資訊與各種行政地圖資訊 例如: 直轄市、縣市界線(TWD97經緯度) 鄉鎮市區界線(TWD97經緯度) | 政府資料開放平臺: https://data

WeselyOng 12 Sep 27, 2022
Using SQLAlchemy with spatial databases

GeoAlchemy GIS Support for SQLAlchemy. Introduction GeoAlchemy is an extension of SQLAlchemy. It provides support for Geospatial data types at the ORM

109 Dec 01, 2022
Construct and use map tile grids in different projection.

Morecantile +-------------+-------------+ ymax | | | | x: 0 | x: 1 | | y: 0 | y: 0

Development Seed 67 Dec 23, 2022
Rasterio reads and writes geospatial raster datasets

Rasterio Rasterio reads and writes geospatial raster data. Geographic information systems use GeoTIFF and other formats to organize and store gridded,

Mapbox 1.9k Jan 07, 2023
Python module to access the OpenCage geocoding API

OpenCage Geocoding Module for Python A Python module to access the OpenCage Geocoder. Build Status / Code Quality / etc Usage Supports Python 3.6 or n

OpenCage GmbH 57 Nov 01, 2022
Advanced raster and geometry manipulations

buzzard In a nutshell, the buzzard library provides powerful abstractions to manipulate together images and geometries that come from different kind o

Earthcube Lab 30 Jun 20, 2022
A light-weight, versatile XYZ tile server, built with Flask and Rasterio :earth_africa:

Terracotta is a pure Python tile server that runs as a WSGI app on a dedicated webserver or as a serverless app on AWS Lambda. It is built on a modern

DHI GRAS 531 Dec 28, 2022
A part of HyRiver software stack for handling geospatial data manipulations

Package Description Status PyNHD Navigate and subset NHDPlus (MR and HR) using web services Py3DEP Access topographic data through National Map's 3DEP

Taher Chegini 5 Dec 14, 2022
Obtain a GNSS position fix from an 11-millisecond raw GNSS signal snapshot

Obtain a GNSS position fix from an 11-millisecond raw GNSS signal snapshot without any prior knowledge about the position of the receiver and only coarse knowledge about the time.

Jonas Beuchert 2 Nov 17, 2022
Python bindings and utilities for GeoJSON

geojson This Python library contains: Functions for encoding and decoding GeoJSON formatted data Classes for all GeoJSON Objects An implementation of

Jazzband 763 Dec 26, 2022
Raster processing benchmarks for Python and R packages

Raster processing benchmarks This repository contains a collection of raster processing benchmarks for Python and R packages. The tests cover the most

Krzysztof Dyba 13 Oct 24, 2022
Simple CLI for Google Earth Engine Uploads

geeup: Simple CLI for Earth Engine Uploads with Selenium Support This tool came of the simple need to handle batch uploads of both image assets to col

Samapriya Roy 79 Nov 26, 2022
WebGL2 powered geospatial visualization layers

deck.gl | Website WebGL2-powered, highly performant large-scale data visualization deck.gl is designed to simplify high-performance, WebGL-based visua

Vis.gl 10.5k Jan 08, 2023
geobeam - adds GIS capabilities to your Apache Beam and Dataflow pipelines.

geobeam adds GIS capabilities to your Apache Beam pipelines. What does geobeam do? geobeam enables you to ingest and analyze massive amounts of geospa

Google Cloud Platform 61 Nov 08, 2022
Focal Statistics

Focal-Statistics The Focal statistics tool in many GIS applications like ArcGIS, QGIS and GRASS GIS is a standard method to gain a local overview of r

Ifeanyi Nwasolu 1 Oct 21, 2021