Bioinformatics tools and resources for immunology

Trainer: Anna Lorenc

Overview: In this session, the trainer will review the available resources and tools (accompanied by a list of links) and how to stay abreast of new developments in the field. The trainer will also briefly describe the practicalities necessary for efficient and future-proof analysis: data and metadata rules, ideas for organising project files, and how to store and share code and data.

Learning outcome
By the end of this session you will be able to:

• Access immunology-related tools and bioinformatic resources
• Recognise key conditions for accessing and maintaining resources for use in research
• Identify the importance of file system and project organisation structure

Materials:

• Presentation slides

Following is a collection useful links:

Single cell -omics

• scrna-tools catalogue of tools for analysing single-cell RNA sequencing data, from the Zappia&Theis paper
• awesome-single-cell List of software packages (and the people developing these methods) for single-cell data analysis, including RNA-seq, ATAC-seq, etc.
• Seurat form Satija lab Vignettes, tutorials
• sc-verse – Python packages for sc scvi-tools, scanpy etc

AIRR (Adaptive Immune Repertoires) – MHC – epitope

• IMGT TCR/BCR references + tools, human + other species
• HLA reference References + tools
• Immcantation Portal with tools to work with AIRR data (BCR oriented)
• MIXCR extract TCR/BCR sequences from targeted sequencing or RNAseq
• TRUST4 extract TCR sequences from targeted sequencing or RNAseq
• VDJdb curated database of TCRs with known specificities
• Olga compute probability of generation of specific V-(D)-J combinations in TCR/BCR
• VDJserver Online analysis of AIRR data
• iReceptor federation of community repositories with AIRR data
• ImmuneAccess repository + online tools for TCR/BCR data sequenced by Adaptive Biotechnologies
• TCRdb TCR database – tissues, diseases, cell types
• McPass-TCR database of pathology related TCRs
• Antibody bioinformatics Tools & references from Andrew C R Martin’s Group at UCL
• IEDB – The Immune Epitope Database A repository of web-based tools for the prediction and analysis of immune epitopes, also experimental datasets
• immuneML machine learning platform for AIRR data

Other immune-specific

• ImmPort immune projects data sharing (NIH) – datasets, tools, resources, tutorials
• ImmGen portal for mouse immunology – gene expression, microRNA, chromatin, gene modules… 2022 is their T cell year!
• FlowRepository repository for flow cytometry data

Gene/protein expression in immune (and other) cells

• DICE Database of Immune Cell Expression, Expression quantitative trait loci (eQTLs) and Epigenomics, bulk and single cell
• proteinatlas – mapping RNA/protein expression across tissues, cells and pathologies

General

• Bioconductor R for life sciences – hub for packages, tutorials, workflows, courses etc.
• introduction to Docker – software carpentry lesson about how to use Docker
• Bioconda repository of conda installs for thousands of bioinformatics packages. With recipes for complicated installs, tutorials