Workflows

What is a Workflow?
301 Workflows visible to you, out of a total of 324

gSpreadComp: Streamlining Microbial Community Analysis for Resistance, Virulence, and Plasmid-Mediated Spread

Overview

gSpreadComp is a UNIX-based, modular bioinformatics toolkit designed to streamline comparative genomics for analyzing microbial communities. It integrates genome annotation, gene spread calculation, plasmid-mediated horizontal gene transfer (HGT) detection and resistance-virulence ranking within the analysed microbial community to help researchers identify potential ...

Type: Shell Script

Creator: Jonas Kasmanas

Submitter: Jonas Kasmanas

DOI: 10.48546/workflowhub.workflow.1340.3

Code for the high risk autism phenotype paper

MIT license

Much of the code in this repo originated from ASD High Risk Endophenotype Code Supplement and was written by Sebastian Urchs and Hien Nguyen.

Data availability

All data to reproduce the analysis can be downloaded from DOI ...

Work-in-progress

AnnoAudit - Annotation Auditor

AnnoAudit is a robust Nextflow pipeline designed to evaluate the quality of genomic annotations through a multifaceted approach.

Overview of the workflow

The workflow assess the annotation quality based on different criteria:

  • Protein evidence support
  • RNASeq evidence support
  • Statistics of the predictions (i.e., gene length, exon number, etc.)
  • Ortholog analysis (BUSCO, OMArk)

Input data

  • Reference genome genome.[.fna, .fa, .fasta]
  • Annotation ...

Type: Nextflow

Creator: Phuong Doan

Submitter: Phuong Doan

DOI: 10.48546/workflowhub.workflow.1330.1

Stable

Prostate cancer classification workflow

This workflow segments tissue regions and classifies prostate cancer on H&E whole slide images, using AI. It consists of three steps:

  1. low-resolution tissue segmentation to select areas for further processing;

  2. high-resolution tissue segmentation to refine borders - it uses step 1 as input;

  3. high-resolution normal/cancer classification - it uses step 1 as input.

Type: Common Workflow Language

Creator: Mauro Del Rio

Submitter: Simone Leo

Stable

Tissue segmentation workflow

This workflow performs tissue segmentation on H&E whole slide images using AI.

Type: Common Workflow Language

Creator: Mauro Del Rio

Submitter: Simone Leo

PISAD - Phsaed Intraspecies Sample Anomalies Detection tool

Summary

We developed PISAD, a tool designed to detect anomalies in cohort samples without requiring reference information. It is primarily divided into two stages. Stage 1: We select low-error data from the cohort and conduct reference-free SNP calling to construct a variant sketch. Stage 2: By comparing the k-mer counts of other cohort data to the variant sketch, we infer the relationships between the sample and other samples to ...

Type: Argo Workflow

Creator: zhantian xu

Submitter: zhantian xu

DOI: 10.48546/workflowhub.workflow.1322.1

REFLOW is a workflow manager tool designed to streamline and automate tasks related to renewable energy potential analyses. It is built with Luigi and provides an automated, robust framework for data acquisition, processing, land/sea eligibility analysis, technology placements, simulations and visualizations. It is build with transparency and reproducibility in mind.

Type: Python

Creators: None

Submitter: Tristan Pelser

Stable

Lin_X_NFDI4BIOIMAGE

FAIR Statistics Aggregator for DOIs

Table of Contents

  1. Introduction
  2. Features
  3. Requirements
  4. Installation
  5. Usage
  6. Output
  7. Limitations
  8. License

Introduction

This repository hosts a prototype tool designed to analyze and aggregate FAIR (Findable, Accessible, Interoperable, and Reusable) statistics for a list ...

Type: Python

Creators: None

Submitter: SaibotMagd magd

Deprecated

Lin_X_NFDI4BIOIMAGE

RDM_system_connector

WARNING

This is a proof of concept, it has not been decided whether it will be developed into a fully functional tool. Feedback is therefore essential, especially as it is unclear whether this type of tool is useful at all, and if so, which parts, as the concept consists of many different parts. (source code readme:

Type: Python

Creators: None

Submitter: SaibotMagd magd

The workflow starts with selecting KLF4 as the search term. Gene sets with set labels containing KLF4 were queried from Enrichr[1]. Identified matching terms from the ENCODE TF ChIP-seq 2015[2] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for ENCODE_TF_ChIP-seq_2015. Identified matching terms from the ChEA 2022[4] library were assembled into a collection of gene sets. A GMT was extracted from the Enrichr results for ChEA_2022. Identified ...

Type: Unrecognized workflow type

Creator: Playbook Partnership NIH CFDE

Submitter: Daniel Clarke

DOI: 10.48546/workflowhub.workflow.1239.2

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