TeSS Training eSupport System

Identifier mapping with Cytoscape

This vignette will show you how to map or translate identifiers from one database (e.g., Ensembl) to another (e.g, Entrez Gene). This is a common requirement for data analysis. In the context of Cytoscape, for example, identifier mapping is needed when you want to import data to overlay on a...

Keywords: ELIXIR RIR, BridgeDb

Identifier mapping with Cytoscape http://cytoscape.org/cytoscape-automation/for-scripters/R/notebooks/Identifier-mapping.nb.html http://tess.elixir-uk.org/materials/identifier-mapping-with-cytoscape This vignette will show you how to map or translate identifiers from one database (e.g., Ensembl) to another (e.g, Entrez Gene). This is a common requirement for data analysis. In the context of Cytoscape, for example, identifier mapping is needed when you want to import data to overlay on a network but you don’t have matching keys. Alex Pico ELIXIR RIR, BridgeDb

BridgeDb-Matlab Usage Instructions

Instructions on how to install and use the BridgeDb functionality in Matlab.

Keywords: ELIXIR RIR, BridgeDb

BridgeDb-Matlab Usage Instructions https://github.com/bridgedb/BridgeDb-matlab http://tess.elixir-uk.org/materials/bridgedb-matlab-usage-instructions Instructions on how to install and use the BridgeDb functionality in Matlab. Denise Slenter ELIXIR RIR, BridgeDb

BridgeDbR Tutorial

This tutorial describes how to use the BridgeDbR package for identifier mapping.

Keywords: ELIXIR RIR, BridgeDb

BridgeDbR Tutorial https://bioconductor.org/packages/devel/bioc/vignettes/BridgeDbR/inst/doc/tutorial.html http://tess.elixir-uk.org/materials/bridgedbr-tutorial-ce581787-b018-4a34-b161-5ed1b9cc8902 This tutorial describes how to use the BridgeDbR package for identifier mapping. Egon Willighagen ELIXIR RIR, BridgeDb

How to install and load the Identifier Mapping Service with data needed for gene-to-variant and variant-to-gene

Tutorial describing how a BridgeDb Identifier Mapping Database (IMS) service can be started and used for gene-variant mapping.

Scientific topics: Genomics, Genetic variation

Keywords: ELIXIR RIR, BridgeDb

Resource type: Tutorial

How to install and load the Identifier Mapping Service with data needed for gene-to-variant and variant-to-gene https://bigcat-um.github.io/BridgeDbVariantDatabase/Local_BridgeDb_IMS_installation.html http://tess.elixir-uk.org/materials/how-to-install-and-load-the-identifier-mapping-service-with-data-needed-for-gene-to-variant-and-variant-to-gene Tutorial describing how a BridgeDb Identifier Mapping Database (IMS) service can be started and used for gene-variant mapping. Friederike Ehrhart Jonathan Mélius Egon Willighagen Genomics Genetic variation ELIXIR RIR, BridgeDb Biologists

#metawinterschool contribution by BiGCaT

Training material from the denBI-organized Metabolomics Winterschool 2018, discussing identifier mapping and pathway analysis.

Scientific topics: Metabolomics

Keywords: Metabolomics, Identifiers, ELIXIR RIR, BridgeDb

Resource type: Tutorial

#metawinterschool contribution by BiGCaT https://egonw.github.io/metawinterschool-bigcat/ http://tess.elixir-uk.org/materials/metawinterschool-contribution-by-bigcat Training material from the denBI-organized Metabolomics Winterschool 2018, discussing identifier mapping and pathway analysis. Egon Willighagen Metabolomics Metabolomics, Identifiers, ELIXIR RIR, BridgeDb Biologists

BridgeDbR Tutorial

Bioconductor Vignette on how to use BridgeDb in the R environment for identifier mapping for genes, proteins, and metabolites.

Keywords: ELIXIR RIR, BridgeDb

Resource type: Tutorial, Vignette

BridgeDbR Tutorial https://bioconductor.org/packages/release/bioc/vignettes/BridgeDbR/inst/doc/tutorial.html http://tess.elixir-uk.org/materials/bridgedbr-tutorial Bioconductor Vignette on how to use BridgeDb in the R environment for identifier mapping for genes, proteins, and metabolites. Egon Willighagen ELIXIR RIR, BridgeDb Biologists Chemists

Working Remotely

Working Remotely from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/07-ssh.md.

Keywords: Extras

Working Remotely https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/07-ssh.md http://tess.elixir-uk.org/materials/working-remotely-ef26eae5-c8f2-4ad5-9622-3732cafbbe33 Working Remotely from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/07-ssh.md. Extras Novice

Permissions

Permissions from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/05-permissions.md.

Keywords: Extras

Permissions https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/05-permissions.md http://tess.elixir-uk.org/materials/permissions-ec9e2168-7558-4aef-b417-1627204b2c2f Permissions from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/05-permissions.md. Extras Novice

Code Review

Code Review from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/03-review.md.

Keywords: Extras

Code Review https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/03-review.md http://tess.elixir-uk.org/materials/code-review Code Review from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/03-review.md. Extras Novice

Shell Variables

Shell Variables from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/06-shellvar.md.

Keywords: Extras

Shell Variables https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/06-shellvar.md http://tess.elixir-uk.org/materials/shell-variables Shell Variables from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/06-shellvar.md. Extras Novice

Exceptions

Exceptions from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/08-exceptions.md.

Keywords: Extras

Exceptions https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/08-exceptions.md http://tess.elixir-uk.org/materials/exceptions Exceptions from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/08-exceptions.md. Extras Novice

Forking a Repository

Forking a Repository from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/02-forking.md.

Keywords: Extras

Forking a Repository https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/02-forking.md http://tess.elixir-uk.org/materials/forking-a-repository Forking a Repository from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/02-forking.md. Extras Novice

Numbers

Numbers from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/09-numbers.md.

Keywords: Extras

Numbers https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/09-numbers.md http://tess.elixir-uk.org/materials/numbers Numbers from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/09-numbers.md. Extras Novice

Branching in Git

Branching in Git from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/01-branching.md.

Keywords: Extras

Branching in Git https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/01-branching.md http://tess.elixir-uk.org/materials/branching-in-git Branching in Git from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/01-branching.md. Extras Novice 2013-08-22

Manual Pages

Manual Pages from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/04-man.md.

Keywords: Extras

Manual Pages https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/04-man.md http://tess.elixir-uk.org/materials/manual-pages Manual Pages from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/04-man.md. Extras Novice

Why I Teach

Why I Teach from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/10-why.md.

Keywords: Extras

Why I Teach https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/10-why.md http://tess.elixir-uk.org/materials/why-i-teach Why I Teach from https://github.com/swcarpentry/bc/tree/gh-pages/novice/extras/10-why.md. Extras Novice

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