inspectro-nf

https://github.com/open2c/inspectro-nf

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
✓
Academic publication links
Links to: zenodo.org
○
Academic email domains
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (12.3%) to scientific vocabulary

Last synced: 6 months ago · JSON representation ·

Repository

Basic Info

Host: GitHub
Owner: open2c
Language: Python
Default Branch: main
Size: 146 KB

Statistics

Stars: 7
Watchers: 8
Forks: 2
Open Issues: 1
Releases: 1

Created almost 3 years ago · Last pushed over 2 years ago

Metadata Files

Readme Citation

Inspectro

Introduction

Diagram of Inspectro pipeline

Inspectro is a bioinformatics pipeline that characterizes long-range interaction profiles in Hi-C maps by spectral decomposition. The pipeline is built using Nextflow, a workflow tool that enables easy installation and reproducibility of the pipeline through Docker containers.

This pipeline (v1.2) supports S3 files for bigwig/bigbed tracks.

Note: Local files are not currently supported.

Future update: Adding iGenomes, which will provide the option to use your own fasta file or one provided by iGenomes for the genome of your choice.

Quick Start and Usage

Install Nextflow (>=21.10.3)
Install Docker to implement environment for pipeline reproducibility. Build the Docker image: docker build -t open2c/inspectrov1.2:latest ./docker
Place supplementary tab-delimited bigwig file with a header in data/track_metadata.tsv to include in graphical outputs. The following columns must be included:

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 absolute path to the file

Add supplementary bigwig track names, sample name and genome assembly name to the params.yml file.
Finally, you can run the pipeline using:

bash nextflow run main.nf \ --config params.yml \ --genome <FASTA_file> \ --meta track_metadata.tsv \ --outdir <OUTDIR> \ --blacklist <blacklist_file> \ --mcool <mcool_file> \ -profile docker

Credits

Tarishi Pathak, Aleksandra Galitsyna, George Spracklin, Nezar Abdennur

Citation

bibtex @article{spracklin2022diverse, title={Diverse silent chromatin states modulate genome compartmentalization and loop extrusion barriers}, author={Spracklin, George and Abdennur, Nezar and Imakaev, Maxim and Chowdhury, Neil and Pradhan, Sriharsa and Mirny, Leonid A and Dekker, Job}, journal={Nature Structural \& Molecular Biology}, pages={1--14}, year={2022}, publisher={Nature Publishing Group} }

Owner

Name: Open Chromosome Collective
Login: open2c
Kind: organization
Email: open.chromosome.collective@gmail.com

Website: https://open2c.github.io/
Repositories: 14
Profile: https://github.com/open2c

Citation (CITATION.cff)

cff-version: 1.1.0
message: "If you use this software, please cite it as below."
authors:
  - given-names: Nezar
    family-names: Abdennur
    orcid: "https://orcid.org/0000-0001-5814-0864"
  - given-names: Tarishi
    family-names: Pathak
  - given-names: George
    family-names: Spracklin
  - given-names: Aleksandra
    family-names: Galitsyna
  - given-names: Garrett
    family-names: Ng
  - given-names: Thomas
    family-names: Reimonn
title: inspectro-nf
version: v0.1.0
date-released: 2023-09-25

GitHub Events

Total

Last Year

Issues and Pull Requests

Last synced: 11 months ago

All Time

Total issues: 0
Total pull requests: 13
Average time to close issues: N/A
Average time to close pull requests: 2 days
Total issue authors: 0
Total pull request authors: 4
Average comments per issue: 0
Average comments per pull request: 0.23
Merged pull requests: 11
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science