Workflows

What is a Workflow?
422 Workflows visible to you, out of a total of 465
Stable

cfDNA-Flow

1. Overview

cfDNA-Flow facilitates the accurate and reproducible analysis of cfDNA WGS data. It offers various preprocessing options to accommodate different experimental setups and research needs in the field of liquid biopsies.

2. Preprocessing options

2.1 Trimming Options

cfDNA-Flow provides the flexibility to either trim or not trim the input reads based on the user's requirements. Trimming removes low-quality bases, which can impact downstream analyses.

2.2 Reference

...

Work-in-progress

🧬 Click-qPCR 🧬

An ultra-simple tool for interactive qPCR data analysis developed with R and Shiny.

日本語版のユーザーガイドはこちら (Read this document in Japanese)

Overview

Click-qPCR is a user-friendly Shiny web application designed for the straightforward analysis of real-time quantitative PCR (qPCR) data.

This tool is readily accessible via a web browser at , requiring no local installation for end-users.

It allows users to upload their Cq (quantification cycle) values, perform ΔCq ...

Type: Unrecognized workflow type

Creators: Azusa Kubota, Atsushi Tajima

Submitter: Azusa Kubota

Stable

The Spatial Transcriptomics analysis workflow for Xenium data from the PATH2XNAT project tested on the non-diseased lung dataset from 10X genomics. The analysis workflow written in R and executed in the interactive RStudio environment consists of visualizations, clustering, feature selection and cluster annotation.

Training materials elaborating on this analysis workflows can be found in this GitHub repository: https://github.com/HCGB-IGTP/PATH2XNAT/tree/main.

This workflow was developed in the ...

Type: Galaxy

Creators: None

Submitter: Myrthe van Baardwijk

Stable

Colorectal-cancer-detection-using-ColoPola-dataset

Methods

We trained and tested three models from scratch (CNN, CNN_2 and EfficientFormerV2) and two pretrained models (DenseNet121 and EfficientNetV2-m) to classify the colorectal cancer using the ColoPola dataset.

ColoPola dataset

The dataset consists of 572 slices (specimens) with 20,592 images. There are 284 cancer samples and 288 normal samples. This dataset can download from Zenodo repository. ...

Type: Python

Creators: Thi-Thu-Hien Pham, Thao-Vi Nguyen, The-Hiep Nguyen, Quoc-Hung Phan, Thanh-Hai Le

Submitter: Thanh-Hai Le

DOI: 10.48546/workflowhub.workflow.1797.2

PanGIA: A universal framework for identifying association between ncRNAs and diseases

PanGIA is a deep learning model for predicting ncRNA-disease associations.

Model Architecture

Installation

conda create -n pangia python=3.11 
conda activate pangia 
pip install -r requirements.txt 

Prepare Datasets

The raw data can be downloaded from the following sources:

  • miRNA: The associations between miRNAs and diseases were obtained from the HMDD v4.0 ...

Type: Python

Creators: None

Submitter: qiankunzizairen Liu

GENome EXogenous (GENEX) sequence detection

This is a computational workflow for detecting coordinates of microbial-like or human-like sequences in eukaryotic and procaryotic reference genomes. The workflow accepts a reference genome in FASTA-format and outputs coordinates of microbial-like (human-like) regions in BED-format. The workflow builds a Bowtie2 index of the reference genome and aligns pre-computed microbial (GTDB v.214 or NCBI RefSeq release 213) or human (hg38) pseudo-reads to the ...

Overview

Developmental version of MSC: This github page contains developmental version of R package for Multi-scale clustering (MSC) to perform single-cell transcriptome clustering. The manuscript is currently under review.

Installation:

MEGENA needs to be installed, prior to MSC installation: library(devtools); install_github("songw01/MEGENA");

For installation for developmental github version: library(devtools); install_github("songlabcodes/MSC");

Vignettes [PBMC 8k ...

Type: R markdown

Creator: Won-Min Song

Submitter: Won-Min Song

DOI: 10.48546/workflowhub.workflow.1875.1

MRanalysis is an interactive R Shiny application designed for Mendelian randomization analysis.

MRanalysis

Mendelian randomization (MR) has emerged as a powerful epidemiological method for inferring causal relationships between exposures and outcomes using genome-wide association study (GWAS) summary data. By leveraging instrumental variables (IVs), such as single nucleotide polymorphisms (SNPs), MR can revolutionize our understanding of disease etiology, ...

Type: Docker

Creator: Abao Xing

Submitter: Abao Xing

DOI: 10.48546/workflowhub.workflow.1872.1

Imputation Workflow h3abionet/chipimputation

Nextflow Docker fair-software.eu

Introduction

Imputation is likely to be run ...

Type: Nextflow

Creators: None

Submitter: Takudzwa Musarurwa

Stable

VIsoQLR: an interactive tool for the detection, quantification and fine-tuning of isoforms using long-read sequencing

VIsoQLR is an interactive analyzer, viewer and editor for the semi-automated identification and quantification of known and novel isoforms using long-read sequencing data. VIsoQLR is tailored to thoroughly analyze mRNA expression and maturation in low-throughput splicing assays. This tool takes sequences aligned to a reference, defines consensus splice sites, and quantifies ...

Type: Docker

Creators: None

Submitter: Yolanda Benítez Quesada

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