https://github.com/bioinfotongli/webatlas-pipeline

Science Score: 41.0%

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
○
.zenodo.json file
✓
DOI references
Found 3 DOI reference(s) in README
✓
Academic publication links
Links to: zenodo.org
○
Academic email domains
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (10.9%) to scientific vocabulary

Last synced: 9 months ago · JSON representation ·

Repository

Basic Info

Host: GitHub
Owner: BioinfoTongLI
License: mit
Language: Python
Default Branch: main
Size: 5.99 MB

Statistics

Stars: 0
Watchers: 0
Forks: 0
Open Issues: 0
Releases: 0

Fork of haniffalab/webatlas-pipeline

Created over 3 years ago · Last pushed over 1 year ago

Metadata Files

Readme License Citation

WebAtlas Pipeline

The WebAtlas Pipeline uses Nextflow to process spatial and single-cell experiment data for visualisation in a web browser.

Usage

The pipeline can handle data from h5ad files, tif image files, SpaceRanger, Xenium and MERSCOPE output. It can also generate label image files from data files.

Running the pipeline requires a parameters file that defines configuration options and the data to be processed. Full instructions and parameters definitions for this files are available in the documentation

A parameters file looks like:

```yaml outdir: "/path/to/output/"

args: h5ad: compute_embeddings: "True"

projects: - project: project1 datasets: - dataset: dataset1 data: - datatype: h5ad datapath: /path/to/project1/dataset1/anndata.h5ad - datatype: rawimage datapath: /path/to/project1/dataset1/rawimage.tif - datatype: labelimage datapath: /path/to/project1/dataset1/labelimage.tif

vitessceoptions: spatial: xy: "obsm/spatial" mappings: obsm/Xumap: [0, 1] layout: "simple" ```

The pipeline can then be run like:

sh nextflow run main.nf -params-file /path/to/run-params.yaml -entry Full_pipeline

Parameters file templates are available in the templates directory.

Owner

Name: Tong LI
Login: BioinfoTongLI
Kind: user
Location: Hinxton
Company: Wellcome Sanger Institute

Repositories: 4
Profile: https://github.com/BioinfoTongLI

Citation (CITATION.cff)

cff-version: 1.2.0
type: software
message: "If you use this repo, please cite it"
title: "WebAtlas"
url: "https://github.com/haniffalab/webatlas-pipeline"
doi: 10.5281/zenodo.7405818
authors:
  - family-names: "Li"
    given-names: "Tong"
    orcid: "https://orcid.org/0000-0002-8240-4476"
  - family-names: "Horsfall"
    given-names: "David"
    orcid: "https://orcid.org/0000-0002-8086-812X"
  - family-names: "Basurto-Lozada"
    given-names: "Daniela"
    orcid: "https://orcid.org/0000-0003-3943-8424"
  - family-names: "Prete"
    given-names: "Martin"
    orcid: "https://orcid.org/0000-0002-5946-821X"
  - family-names: "Jessica"
    given-names: "Cox"
    orcid: "https://orcid.org/0000-0002-1109-1679"
  - family-names: "Iolo"
    given-names: "Squires"
    orcid: "https://orcid.org/0000-0002-3424-6354"

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science