• Carpentree test case

    Manual example created as proof of concept for our Carpentree project, created at the #CollabW19 workshop in Loughborough on 3 April 2019

    The lessons referred to are:
    - Programming with Python (PP): http://swcarpentry.github.io/python-novice-inflammation/index.html
    - Plotting and...

  • ChIP-seq workflow

    Basic workflow for ChIP-seq analysis

    Topic: ChIP-seq

  • ChIP-seq workflow (with intermediate data)

    Basic workflow for ChIP-seq analysis

    Topic: ChIP-seq

  • ChIP-seq workflow in Bioconductor

    Basic workflow for ChIP-seq analysis using Bioconductor from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5389943/

    Topic: ChIP-seq

  • EBI metagenomics pipeline 2.0

    EBI metagenomics pipeline 2.0

  • ELIXIR Structural Bioinformatics 2: Exploring protein domains and functional sites

    This training workflow introduces how to search (using query protein sequences or structures) for protein domains, conservation and protein family information, surface and topological interfaces, and possible ligand binding sites.

    It is designed to lead you through the process of finding...

  • ELIXIR Structural Bioinformatics 3: Predicting the effect of mutation on protein function

    This workflow builds on the previous training workflows in this series on building protein models and identifying functional domains or ligand binding sites - and introduces methods to predict how mutations can impact on protein function.

    It is designed to lead you through the process of...

  • EMBER: A practical guide to Bioinformatics

    This practical introduces a range of Web-based databases and tools, allowing their relative strengths and weaknesses to be compared. The practical comprises several modules, each broken down into simple steps.

  • Image analysis

    Imaging (http://edamontology.org/topic_3382)

    Bioimage informatics (EDAM-bioimaging)

  • Meta-pipe


  • Peroxisomal Proteins Detection

    Workflow to identify putative peroxisomal proteins from the FASTA sequence

  • Protein Structure Modelling

    This is the a workflow of protein modelling.

  • READemption

    READemption is a pipeline for the computational evaluation of RNA-Seq data. It was originally developed to process dRNA-Seq reads (as introduced by Sharma et al., Nature, 2010 (Pubmed)) originating from bacterial samples. Meanwhile is has been extended to process data generated in different...

  • RNA-seq summarization with annotated genome

    Basic workflow for RNA-seq analysis to get to a count table.

  • Structural bioinformatics workflow

    A workflow with suggested common stages taken in structural bioinformatics

  • Text mining and annotation

    Natural language processing (http://edamontology.org/topic_0218)

  • Text mining and annotation (more detail)

    Natural language processing (http://edamontology.org/topic_0218)

  • TRUFA RNAseq

    TRUFA (Transcriptomes User-Friendly Analysis) is a free webserver designed to help you perform RNA-seq analysis.

    So far, TRUFA is allowing you to execute the following steps (programs used are specified in the parentheses):

    Reads cleaning:
    Reads quality control (FASTQC)
    Quality trimming...