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19 Collections visible to you, out of a total of 19

Interactive Jupyter Notebooks in combination with Conda environments can be used to generate FAIR (Findable, Accessible, Interoperable and Reusable/Reproducible) biomolecular simulation workflows. The interactive programming code accompanied by documentation, and the possibility to inspect intermediate results with versatile graphical charts and data visualization is very helpful, especially in iterative processes, where parameters might be adjusted to a particular system of interest. This work ...

Maintainers: Genís Bayarri, Adam Hospital

Number of items: 17

Tags: Bioinformatics, BioBB

Collection of workflows used or developed by the EuroScienceGateway project.

Maintainers: Stian Soiland-Reyes, Paul De Geest

Number of items: 10

Tags: Not specified

Collection of de-novo genome assembly workflows written for implementation in Galaxy

Input data should be Oxford Nanopore raw reads plus Illumina WGS reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads

Executing all workflows will output one scaffolded collapsed assembly and the complete QC analyses

Please run the workflows in order: WF0 (there are two, one for ONT, and another one for Illumina that can be used independently for the WGS and HiC reads), WF1, WF2, WF3, WF4

Maintainers: Diego De Panis

Number of items: 5

Tags: Assembly, Bioinformatics, Galaxy, Genomics, Genome assembly, ONT, illumina, Hi-C

Collection of de-novo genome assembly workflows written for implementation in Galaxy

Input data should be Oxford Nanopore raw reads plus Illumina WGS reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads

Executing all workflows will output one scaffolded collapsed assembly and the complete QC analyses

Please run the workflows in order: WF0 (there are two, one for ONT, and another one for Illumina that can be used independently for the WGS and HiC reads), WF1, WF2, WF3, WF4

Maintainers: Diego De Panis

Number of items: 6

Tags: Assembly, Bioinformatics, Galaxy, Genomics, Genome assembly, ONT, illumina, Hi-C

Workflows developed by or used by BY-COVID project.

Maintainers: Stian Soiland-Reyes

Number of items: 0

Tags: Not specified

This collection contains all the pipelines and methods used to generate reference genome assemblies in the Tree of Life department of the Sanger institute

Maintainers: Matthieu Muffato

Number of items: 1

Tags: Not specified

Collection of de-novo genome assembly workflows written for implementation in Galaxy

Input data should be PacBio HiFi reads and Illumina 3-dimensional Chromatin Confirmation Capture (HiC) reads

Executing all workflows will output two scaffolded haplotype assemblies and the complete QC analyses

Please run the workflows in order: WF0 (there are two, one for HiFi and one for Illumina HiC), WF1, WF2, WF3, WF4

Maintainers: Tom Brown, Diego De Panis

Number of items: 6

Tags: Assembly, Bioinformatics, Galaxy, Genomics, Genome assembly, HiFi, Hi-C

This collection houses some scanpy-based scRNAseq workflows on galaxy Australia.

The aim of these workflows is to handle the routine ‘boring’ part of single cell RNAseq data processing. It will produces an ‘AnnData’ object, which can then be used as a base for downstream analysis – either within galaxy or outside of it. AnnData is a standard format used by the ‘scanpy’ python package.

These workflows represent just one way of processing data for a ‘typical’ scRNAseq experiment – there are many ...

Maintainers: Sarah Williams

Number of items: 8

Tags: Not specified

The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for piepline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.

Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html ...

Maintainers: Sarah Williams, Ahmed Mehdi, Original galaxy workflow developers: Saskia Hiltemann, Bérénice Batut, Dave Clements

Number of items: 7

Tags: Not specified

This is a general collection of workflows used by or developed by members of the BGE project.

Maintainers: Stian Soiland-Reyes

Number of items: 0

Tags: Genomics, Biodiversity

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