Cristóbal Gallardo

Former Affiliations

Contributions

The following list includes only slides and tutorials where the individual or organisation has been added to the contributor list. This may not include the sum total of their contributions to the training materials (e.g. GTN css or design, tutorial datasets, workflow development, etc.) unless described by a news post.

Tutorials

• Sequence analysis / Quality Control 🧐
• Sequence analysis / NCBI BLAST+ against the MAdLand 🧐
• Transcriptomics / Genome-wide alternative splicing analysis ✍️ 🧐
• Transcriptomics / Network analysis with Heinz 🧐
• Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana ✍️ 🧐
• Transcriptomics / Reference-based RNA-Seq data analysis 🧐
• Microbiome / Taxonomic Profiling and Visualization of Metagenomic Data 🧐
• Microbiome / Identification of the micro-organisms in a beer using Nanopore sequencing 🧐
• Microbiome / Pathogen detection from (direct Nanopore) sequencing data using Galaxy - Foodborne Edition 🧐
• Microbiome / 16S Microbial analysis with Nanopore data ✍️ 🧐
• Genome Annotation / Genome annotation with Funannotate 🧐
• Genome Annotation / From small to large-scale genome comparison 🧐
• Genome Annotation / Masking repeats with RepeatMasker 🧐
• Metabolomics / Mass spectrometry : GC-MS analysis with metaMS package 🧐
• Foundations of Data Science / Advanced R in Galaxy 🧐
• Teaching and Hosting Galaxy training / Training techniques to enhance learner participation and engagement 🧐
• Teaching and Hosting Galaxy training / Assessment and feedback in training and teachings 🧐
• Teaching and Hosting Galaxy training / Motivation and Demotivation 🧐
• Teaching and Hosting Galaxy training / Train-the-Trainer: putting it all together 🧐
• Using Galaxy and Managing your Data / Rule Based Uploader 🧐
• Using Galaxy and Managing your Data / Group tags for complex experimental designs 🧐
• Using Galaxy and Managing your Data / Understanding Galaxy history system 📝
• Development in Galaxy / Contributing to BioBlend as a developer 🧐
• Assembly / Genome assembly using PacBio data 🧐
• Assembly / Using the VGP workflows to assemble a vertebrate genome with HiFi and Hi-C data ✍️ 🧐
• Assembly / Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step ✍️ 🧐
• Assembly / Chloroplast genome assembly 🧐
• Assembly / ERGA post-assembly QC ✍️ 🧐
• Assembly / Large genome assembly and polishing 🧐
• Assembly / Genome Assembly Quality Control 🧐
• Assembly / Genome Assembly of a bacterial genome (MRSA) sequenced using Illumina MiSeq Data 🧐
• Assembly / An Introduction to Genome Assembly 🧐
• Assembly / Genome Assembly of MRSA from Oxford Nanopore MinION data (and optionally Illumina data) 🧐
• Introduction to Galaxy Analyses / Galaxy Basics for genomics 🧐
• Introduction to Galaxy Analyses / Introduction to Genomics and Galaxy ✍️ 🧐
• Introduction to Galaxy Analyses / A short introduction to Galaxy 🧐
• Imaging / Object tracking using CellProfiler 🧐
• Visualisation / Visualisation with Circos ✍️ 🧐
• Ecology / Metabarcoding/eDNA through Obitools 🧐
• Contributing to the Galaxy Training Material / Principles of learning and how they apply to training and teaching ✍️ 🧐
• Contributing to the Galaxy Training Material / Creating content in Markdown 🧐
• Contributing to the Galaxy Training Material / Design and plan session, course, materials 🧐
• Epigenetics / Formation of the Super-Structures on the Inactive X 🧐
• Variant Analysis / M. tuberculosis Variant Analysis 🧐
• Climate / Pangeo ecosystem 101 for everyone - Introduction to Xarray Galaxy Tools 🧐
• Climate / Pangeo Notebook in Galaxy - Introduction to Xarray 🧐
• Single Cell / Pre-processing of 10X Single-Cell RNA Datasets 🧐
• Single Cell / Pre-processing of 10X Single-Cell ATAC-seq Datasets 🧐
• Single Cell / Analysis of plant scRNA-Seq Data with Scanpy ✍️
• Synthetic Biology / Generating theoretical possible pathways for the production of Lycopene in E.Coli using Retrosynthesis tools 🧐
• Introduction to Galaxy Analyses / Breve introducción a Galaxy - en español 🧐

Slides

• Development in Galaxy / Galaxy from a developer point of view 🧐
• Sequence analysis / Quality Control 🧐
• Sequence analysis / Mapping ✍️ 🧐
• Transcriptomics / Identification of non-canonical ORFs and their potential biological function ✍️ 🧐
• Transcriptomics / Network Analysis with Heinz 🧐
• Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana ✍️ 🧐
• Transcriptomics / Introduction to Transcriptomics 🧐
• Transcriptomics / Integrate and query local datasets and distant RDF data with AskOmics using Semantic Web technologies 🧐
• Microbiome / Introduction to Microbiome Analysis 🧐
• Microbiome / Introduction to metatranscriptomics 🧐
• Genome Annotation / Introduction to Genome Annotation 🧐
• Genome Annotation / High Performance Computing for Pairwise Genome Comparison 🧐
• Metabolomics / Introduction to Metabolomics 🧐
• Metabolomics / Mass spectrometry: LC-MS preprocessing - advanced 🧐
• Teaching and Hosting Galaxy training / Workshop Kickoff 🧐
• Using Galaxy and Managing your Data / Getting data into Galaxy 🧐
• Development in Galaxy / Galaxy Interactive Environments 🧐
• Development in Galaxy / Tool Dependencies and Containers 🧐
• Development in Galaxy / Galaxy Code Architecture 🧐
• Development in Galaxy / Tool development and integration into Galaxy 🧐
• Development in Galaxy / Tool Shed: sharing Galaxy tools 🧐
• Development in Galaxy / Galaxy Interactive Tours 🧐
• Development in Galaxy / Tool Dependencies and Conda 🧐
• Development in Galaxy / Visualizations: JavaScript Plugins 🧐
• Development in Galaxy / Galaxy Webhooks 🧐
• Development in Galaxy / Generic plugins 🧐
• Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads ✍️ 🧐
• Assembly / An introduction to get started in genome assembly and annotation 🧐
• Assembly / Unicycler Assembly 🧐
• Assembly / Genome assembly quality control. 🧐
• Assembly / An Introduction to Genome Assembly 🧐
• Assembly / De Bruijn Graph Assembly 🧐
• Introduction to Galaxy Analyses / Options for using Galaxy 🧐
• Introduction to Galaxy Analyses / Introduction to Galaxy 🧐
• Introduction to Galaxy Analyses / A Short Introduction to Galaxy 🧐
• Imaging / Nucleoli Segmentation
  &
  Feature Extraction
  using CellProfiler 🧐
• Visualisation / Visualisations in Galaxy 🧐
• Contributing to the Galaxy Training Material / Contributing with GitHub via command-line 🧐
• Contributing to the Galaxy Training Material / Creating Slides 🧐
• Epigenetics / Introduction to ChIP-Seq data analysis 🧐
• Epigenetics / Introduction to DNA Methylation data analysis 🧐
• Epigenetics / Introduction to ATAC-Seq data analysis 🧐
• Epigenetics / ChIP-seq data analysis 🧐
• Epigenetics / EWAS Epigenome-Wide Association Studies Introduction 🧐
• Variant Analysis / Introduction to Variant analysis 🧐
• Statistics and machine learning / Feedforward neural networks (FNN) Deep Learning - Part 1 🧐
• Statistics and machine learning / Convolutional neural networks (CNN) Deep Learning - Part 3 🧐
• Climate / Pangeo ecosystem 101 for everyone 🧐
• Climate / The Pangeo ecosystem 🧐
• Single Cell / An introduction to scRNA-seq data analysis 🧐
• Proteomics / Introduction to proteomics, protein identification, quantification and statistical modelling 🧐
• Galaxy Server administration / Galaxy on the Cloud 🧐
• Galaxy Server administration / Galaxy from an administrator's point of view 🧐
• Galaxy Server administration / Docker and Galaxy 🧐
• Galaxy Server administration / Terraform 🧐
• Introduction to Galaxy Analyses / Una Breve Introducción a Galaxy 🧐

FAQs

• Could I use a different p-adj value for filtering differentially expressed genes?
• Can I use alternative tools for the Quantification step?

Video Recordings

• Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana 💬
• Transcriptomics / Whole transcriptome analysis of Arabidopsis thaliana 💬 🗣
• Development in Galaxy / Creating Galaxy tools from Conda Through Deployment 💬 🗣
• Assembly / Unicycler assembly of SARS-CoV-2 genome with preprocessing to remove human genome reads 🗣
• Galaxy Server administration / Use Apptainer containers for running Galaxy jobs 💬

GitHub Activity

github Issues Reported

65 Merged Pull Requests

See all of the github Pull Requests and github Commits by Cristóbal Gallardo.

• Genome-wide alternative splicing: add slides and fix typos
  transcriptomics
• Learning principles training: fix references
  contributing
• Genome-wide alternative splicing training v.2.0
  review-needed
  transcriptomics
• Add as contributor to Learning principles training
  contributing
• Alternative splicing training: improve introduction
  transcriptomics

Reviewed 74 PRs

We love our community reviewing each other's work!

• Small updates from feedback from the last workshop
  metagenomics
• Update ChIP-Seq tutorial with latest tool versions and links
  epigenetics
• Genome-wide alternative splicing: add slides and fix typos
  transcriptomics
• github Auto Compress Images
• ERGA post-assembly QC training
  template-and-tools
  assembly

News

External Links

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