Workflows
What is a Workflow?Filters
The workflow takes trimmed HiC paired-end reads collection, and Pri/Alt assemblies to produce a scaffolded primary assembly (and alternate contigs) using YaHS. It also runs Pretext and all the QC analyses (gfastats, BUSCO, and Merqury).
The workflow takes a long reads collection (HiFi, or ONT also possible now), and max coverage depth (calculated from WF1) to run Hifiasm in solo mode. It produces a Pri/Alt assembly, Bandage plots, and runs all the QC analysis (gfastats, BUSCO, and Merqury).
SeuratExtend: An Enhanced Toolkit for scRNA-seq Analysis
Overview
SeuratExtend
is an R package designed to provide an improved and easy-to-use toolkit for scRNA-seq analysis and visualization, built upon the Seurat object. While Seurat
is a widely-used tool in the R community that offers a foundational framework for scRNA-seq analysis, it has limitations when it comes to more advanced analysis and customized visualization. SeuratExtend
expands upon Seurat
by offering an array of
...
Application that perform the multiplication between matrices.
This workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract, filter, align and fill gapand the possibility to annotate isotopes, adducts and fragments using the CAMERA R package (Kuhl, C 2012).
Gene_fetch
This tool fetches gene sequences from NCBI databases based on taxonomy IDs (taxids) or taxonomic information. It can retrieve both protein and nucleotide sequences for various genes, including protein-coding genes (e.g., cox1, cytb, rbcl, matk) and rRNA genes (e.g., 16S, 18S).
Feature highlight
- Fetch protein and/or nucleotide sequences from NCBI GenBank database.
- Handles both direct nucleotide sequences and protein-linked nucleotide searches (CDS extraction includes fallback ...
Annual percentage Change for population in Germany (1950 - 2025)
This workflow run was executed on Galaxy (Workflow Rerun Information)
Workflow: Climate Stripes
Execution Status: scheduled
Executed: 2025-05-27 14:14:07.240149
Workflow Inputs
Formal Input Definitions
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Germany-Population-Annual--Change-2025-05-27-15-17.csv (File)
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Column name to use for plotting (Text)
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Plot Title (Text)
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nxsplit (Integer)
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Description: Number of values per intervals
...
EOSC4Cancer_D2.2
Galaxy workflow used for EOSC4Cancer D2.2 - Analytical methods for data extraction, processing and sharing using biomedical images - demonstrator
Link to deliverable report on Zenodo:
Type: Galaxy
Creators: Jeanne Chèneby, Hakim Achterberg, Dario Longo, Francesco Gammaraccio, Robin Navest
Submitter: Robin Navest