Expertise: Bioinformatics
Tools: CWL, Genomics, Python, R, Transcriptomics, Jupyter notebook
Hiroshima University, Graduate School of Integrated Sciences for life, Laboratory of Genome Informatics, Ph.D student GitHub: https://github.com/yonesora56
Expertise: Traslational Research
Tools: PCR, Transcriptomics, Microarray analysis, Animal models
Remedios Otero Candelera began her research career with clinical work and has progressively participated in translational research projects until she became the leader of the Respiratory Diseases group of the Cardiovascular, Respiratory and other Systemic Pathology Area at the Institute of Biomedicine of Seville on the campus of the Virgen del Rocío University Hospital. He also coordinates the research group of the Andalusian Plan for Research, Development and Innovation (PAIDI) (CTS551): Research ...
Expertise: Genomics, Metagenomics, NGS, Python, evolution
Tools: Genomics, Python, Snakemake, Transcriptomics
Expertise: Bioinformatics
Tools: R, Transcriptomics
Expertise: Bioinformatics, Genomics, Metagenomics, Data Management
Tools: CWL, Jupyter notebook, Nextflow, Molecular Biology, Workflows, Microbiology, Transcriptomics, Perl, Python, R
Expertise: Bioinformatics, Computer Science, Data Management, Genetics, Genomics, Machine Learning, Metagenomics, NGS, Scientific workflow developement, Software Engineering
Tools: Databases, Galaxy, Genomics, Jupyter notebook, Machine Learning, Nextflow, nf-core, PCR, Perl, Python, R, rtPCR, Snakemake, Transcriptomics, Virology, Web, Web services, Workflows
Dad, husband and PhD. Scientist, technologist and engineer. Bibliophile. Philomath. Passionate about science, medicine, research, computing and all things geeky!
Teams: MAB - ATGC
Organizations: Centre National de la Recherche Scientifique (CNRS)

Expertise: Bioinformatics, Genomics, algorithm, Machine Learning, Metagenomics, NGS, Computer Science
Tools: Transcriptomics, Genomics, Python, C/C++, Web services, Workflows
Teams: Harkany Lab
Organizations: Medical University of Vienna

Expertise: Systems Biology, Bioengineering, Bioinformatics, Neuroscience
Tools: Workflows, Machine Learning, Transcriptomics
Toward data-driven genome breeding (digital breeding), we are developing data analysis infrastructure technology essential for genome editing, focusing on gene function analysis using bioinformatics called BioDX.
Space: Hiroshima workflow community
Public web page: https://bonohu.hiroshima-u.ac.jp/index_en.html
Organisms: Not specified
Visualization of RNA-Seq results with heatmap2
Associated Tutorial
This workflows is part of the tutorial Visualization of RNA-Seq results with heatmap2, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
**Tutorial ...
Identify upregulated miRNAS and analyze potential targets in downregulated genes.
Associated Tutorial
This workflows is part of the tutorial Whole transcriptome analysis of Arabidopsis thaliana, available in the GTN
Thanks to...
Tutorial Author(s): Cristóbal Gallardo, ...
roscoff hackathon
Associated Tutorial
This workflows is part of the tutorial De novo transcriptome assembly, annotation, and differential expression analysis, available in the GTN
Thanks to...
Tutorial Author(s): Anthony Bretaudeau, [Gildas Le ...
Reference-based RNA-Seq data analysis
Associated Tutorial
This workflows is part of the tutorial Reference-based RNA-Seq data analysis, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Bérénice Batut, ...
Reference-based RNA-Seq data analysis
Associated Tutorial
This workflows is part of the tutorial Reference-based RNA-Seq data analysis, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Workflow Author(s): Bérénice Batut, ...
Reference-based RNA-Seq data analysis
Associated Tutorial
This workflows is part of the tutorial Reference-based RNA-Seq data analysis, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Uses ...
Visualization of RNA-Seq results with Volcano Plot
Associated Tutorial
This workflows is part of the tutorial Visualization of RNA-Seq results with Volcano Plot, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes ...
CLIP-Seq data analysis from pre-processing to motif detection
Associated Tutorial
This workflows is part of the tutorial CLIP-Seq data analysis from pre-processing to motif detection, available in the GTN
Thanks to...
Tutorial Author(s): Florian Heyl, [Daniel ...
RNA-seq counts to genes
Associated Tutorial
This workflows is part of the tutorial 2: RNA-seq counts to genes, available in the GTN
Thanks to...
Tutorial Author(s): Maria Doyle, Belinda Phipson, ...
RNA-seq genes to pathways
Associated Tutorial
This workflows is part of the tutorial 3: RNA-seq genes to pathways, available in the GTN
Thanks to...
Tutorial Author(s): Maria Doyle, Belinda Phipson ...
rna-seq-reads-to-counts
Associated Tutorial
This workflows is part of the tutorial 1: RNA-Seq reads to counts, available in the GTN
Thanks to...
Tutorial Author(s): Maria Doyle, Belinda Phipson, ...
RNA-Seq reads to counts
Associated Tutorial
This workflows is part of the tutorial 1: RNA-Seq reads to counts, available in the GTN
Thanks to...
Tutorial Author(s): Maria Doyle, Belinda Phipson, ...
De novo transcriptome reconstruction with RNA-Seq
Associated Tutorial
This workflows is part of the tutorial De novo transcriptome reconstruction with RNA-Seq, available in the GTN
Thanks to...
Tutorial Author(s): Mallory Freeberg, [Mo ...
RNA-RNA interactome analysis using ChiRA tool suite
Associated Tutorial
This workflows is part of the tutorial RNA-RNA interactome data analysis, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
Tutorial Author(s): ...
Network analysis with Heinz
Associated Tutorial
This workflows is part of the tutorial Network analysis with Heinz, available in the GTN
Thanks to...
Tutorial Author(s): Chao Zhang
[![gtn star logo followed by the word ...
This workflow completes the second part of the sRNA-seq tutorial from transcript quantification through differential abundance testing.
Associated Tutorial
This workflows is part of the tutorial Differential abundance testing of small RNAs, available in the GTN
Thanks to...
Tutorial Author(s): [Mallory ...
This workflow completes the first part of the small RNA-seq tutorial from read pre-processing to trimming.e
Associated Tutorial
This workflows is part of the tutorial Differential abundance testing of small RNAs, available in the GTN
Thanks to...
Tutorial Author(s): Mallory Freeberg ...
Small Non-coding RNA Clustering using BlockClust
Associated Tutorial
This workflows is part of the tutorial Small Non-coding RNA Clustering using BlockClust, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks to...
...
GO Enrichment Analysis Tutorial
Associated Tutorial
This workflows is part of the tutorial GO Enrichment Analysis, available in the GTN
Thanks to...
Tutorial Author(s): IGC Bioinformatics Unit, Maria Doyle ...
Downstream Single-cell RNA Plant analysis with ScanPy
Associated Tutorial
This workflows is part of the tutorial Analysis of plant scRNA-Seq Data with Scanpy, available in the GTN
Thanks to...
Tutorial Author(s): Mehmet Tekman, [Beatriz ...
Workflow for the first half of the "Bulk RNA Deconvolution with MuSiC" tutorial.
Associated Tutorial
This workflows is part of the tutorial Bulk RNA Deconvolution with MuSiC, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy ...
Workflow for the second half of the "Bulk RNA Deconvolution with MuSiC" tutorial.
Implements the "Estimation of cell type proportions with pre-grouping of cell types" section
Associated Tutorial
This workflows is part of the tutorial Bulk RNA Deconvolution with MuSiC, available in the GTN
Features
- Includes [Galaxy Workflow ...
Associated Tutorial
This workflows is part of the tutorial Removing the effects of the cell cycle, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a Galaxy Workflow Report ...
Downstream Single-cell RNA analysis with RaceID
Associated Tutorial
This workflows is part of the tutorial Downstream Single-cell RNA analysis with RaceID, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
Associated Tutorial
This workflows is part of the tutorial Pre-processing of 10X Single-Cell RNA Datasets, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
Single-cell quality control with scater
Associated Tutorial
This workflows is part of the tutorial Single-cell quality control with scater, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
Filter, Plot and Explore Single-cell RNA-seq Data
Associated Tutorial
This workflows is part of the tutorial Filter, plot and explore single-cell RNA-seq data with Scanpy, available in the GTN
Features
- Includes Galaxy Workflow Tests
Thanks
...
Pre-processing of Single-Cell RNA Data
Associated Tutorial
This workflows is part of the tutorial Pre-processing of Single-Cell RNA Data, available in the GTN
Thanks to...
Tutorial Author(s): Mehmet Tekman, [Bérénice ...
Pre-processing of Single-Cell RNA Data
Associated Tutorial
This workflows is part of the tutorial Pre-processing of Single-Cell RNA Data, available in the GTN
Features
- Uses subworkflows
Thanks to...
Tutorial Author(s): [Mehmet ...
Downstream Single-cell RNA Plant analysis with ScanPy
Associated Tutorial
This workflows is part of the tutorial Analysis of plant scRNA-Seq Data with Scanpy, available in the GTN
Features
- Includes Galaxy Workflow Tests
- Includes a [Galaxy Workflow ...
A workflow for performing alignment and phylogeny using protein sequences from the CrusTome database. See crustybase.org/crustome for more information.
Workflow for gene set enrichment analsysis (GSEA) and co-expression analysis (WGCNA) on transcriptomics data to analyze pathways affected in Porto-Sinusoidal Vascular Disease.
Type: Common Workflow Language
Creators: Aishwarya Iyer, Friederike Ehrhart
Submitter: Aishwarya Iyer
SLAMseq analysis using Slamdunk with various T>C conversion quantifications and QC
RASflow: RNA-Seq Analysis Snakemake Workflow
RASflow is a modular, flexible and user-friendly RNA-Seq analysis workflow.
RASflow can be applied to both model and non-model organisms. It supports mapping RNA-Seq raw reads to both genome and transcriptome (can be downloaded from public database or can be homemade by users) and it can do both transcript- and gene-level Differential Expression Analysis (DEA) when transcriptome is used as mapping reference. It requires little programming skill for ...
Workflow for Creating a large disease network from various datasets and databases for IBM, and applying the active subnetwork identification method MOGAMUN.
Type: Common Workflow Language
Creators: Daphne Wijnbergen, Mridul Johari
Submitter: Daphne Wijnbergen
ERGA Protein-coding gene annotation workflow.
Adapted from the work of Sagane Joye:
https://github.com/sdind/genome_annotation_workflow
Prerequisites
The following programs are required to run the workflow and the listed version were tested. It should be noted that older versions of snakemake are not compatible with newer versions of singularity as is noted here: https://github.com/nextflow-io/nextflow/issues/1659.
conda v 23.7.3
...
prepareChIPs
This is a simple snakemake
workflow template for preparing single-end ChIP-Seq data.
The steps implemented are:
- Download raw fastq files from SRA
- Trim and Filter raw fastq files using
AdapterRemoval
- Align to the supplied genome using
bowtie2
- Deduplicate Alignments using
Picard MarkDuplicates
- Call Macs2 Peaks using
macs2
A pdf of the rulegraph is available here
Full details for each step are given below. Any additional ...
A CWL-based pipeline for processing RNA-Seq data (FASTQ format) and performing differential gene/transcript expression analysis.
On the respective GitHub folder are available:
- The CWL wrappers for the workflow
- A pre-configured YAML template, based on validation analysis of publicly available HTS data
- A table of metadata (
mrna_cll_subsets_phenotypes.csv
), based on the same validation analysis, to serve as an input example for the design of comparisons during differential expression ...
Type: Common Workflow Language
Creators: Konstantinos Kyritsis, Nikolaos Pechlivanis, Fotis Psomopoulos
Submitter: Konstantinos Kyritsis
Genome-wide alternative splicing analysis v.2
This workflow correspond to the Genome-wide alternative splicing analysis training. It allows to analyze isoform switching by making use of IsoformSwitchAnalyzeR.
Workflow for Illumina Quality Control and Filtering
Multiple paired datasets will be merged into single paired dataset.
Summary:
- FastQC on raw data files
- fastp for read quality trimming
- BBduk for phiX and (optional) rRNA filtering
- Kraken2 for taxonomic classification of reads (optional)
- BBmap for (contamination) filtering using given references (optional)
- FastQC on filtered (merged) data
Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default ...
Type: Common Workflow Language
Creators: Bart Nijsse, Jasper Koehorst, Changlin Ke
Submitter: Bart Nijsse
polya_liftover - sc/snRNAseq Snakemake Workflow
A [Snakemake][sm] workflow for using PolyA_DB and UCSC Liftover with Cellranger.
Some genes are not accurately annotated in the reference genome. Here, we use information provide by the [PolyA_DB v3.2][polya] to update the coordinates, then the [USCS Liftover][liftover] tool to update to a more recent genome. Next, we use [Cellranger][cr] to create the reference and count matrix. Finally, by taking advantage of the integrated [Conda][conda] and ...
Flashlite-Trinity contains two workflows that run Trinity on the University of Queensland's HPC, Flashlite. Trinity performs de novo transcriptome assembly of RNA-seq data by combining three independent software modules Inchworm, Chrysalis and Butterfly to process RNA-seq reads. The algorithm can detect isoforms, handle paired-end reads, multiple insert sizes and strandedness. Users can run Flashlite-Trinity on single samples, or smaller samples requiring <500Gb ...
Type: Shell Script
Creators: Tracy Chew, Rosemarie Sadsad, Georgina Samaha, Cali Willet
Submitter: Tracy Chew
Description: Trinity @ NCI-Gadi contains a staged Trinity workflow that can be run on the National Computational Infrastructure’s (NCI) Gadi supercomputer. Trinity performs de novo transcriptome assembly of RNA-seq data by combining three independent software modules Inchworm, Chrysalis and Butterfly to process RNA-seq reads. The algorithm can detect isoforms, handle paired-end reads, multiple insert sizes and strandedness. ...
Type: Shell Script
Creators: Georgina Samaha, Rosemarie Sadsad, Tracy Chew, Matthew Downton, Andrey Bliznyuk, Rika Kobayashi, Ben Menadue, Ben Evans
Submitter: Tracy Chew
ORSON combine state-of-the-art tools for annotation processes within a Nextflow pipeline: sequence similarity search (PLAST, BLAST or Diamond), functional annotation retrieval (BeeDeeM) and functional prediction (InterProScan). When required, BUSCO completness evaluation and eggNOG Orthogroup annotation can be activated. While ORSON results can be analyzed through the command-line, it also offers the possibility to be compatible with BlastViewer or Blast2GO graphical tools.
Type: Nextflow
Creators: Cyril Noel, Alexandre Cormier, Patrick Durand, Laura Leroi, Pierre Cuzin
Submitter: Patrick Durand
A porting of the Trinity RNA assembly pipeline, https://trinityrnaseq.github.io, that uses Nextflow to handle the underlying sub-tasks. This enables additional capabilities to better use HPC resources, such as packing of tasks to fill up nodes and use of node-local disks to improve I/O. By design, the pipeline separates the workflow logic (main file) and the cluster-specific configuration (config files), improving portability.
Based on a pipeline by Sydney Informatics Hub: ...
RNA-RNA interactome analysis using ChiRA tools suite. The aligner used is CLAN.
RNA-RNA interactome analysis using ChiRA tools suite. The aligner used is BWA-MEM.