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19 materials found

Keywords: Shell  or ELIXIR RIR, BridgeDb 

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

BridgeDb-Matlab Usage Instructions

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

Keywords: ELIXIR RIR, BridgeDb

BridgeDbR Tutorial

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

Keywords: 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. It explains how to download the IMS Docker and identifier mapping databases (link sets), load the link sets, and test the web interface.

Scientific topics: Genomics, Genetic variation

Keywords: ELIXIR RIR, BridgeDb

Resource type: Tutorial

#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

BridgeDbR Tutorial

BridgeDb is a combination of an application programming interface (API), library, and set of data files for mapping identifiers for identical objects [1]. Identifier mapping databases are available for gene products and metabolites. This Bioconductor Vignette explains how to use BridgeDb in the R...

Keywords: ELIXIR RIR, BridgeDb

Resource type: Tutorial, Vignette

Filename Expansion

Filename Expansion from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/05-expansion.md.

Keywords: Shell

Job Control

Job Control from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/04-job.md.

Keywords: Shell

Instructor's Guide

Instructor's Guide from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/guide.md.

Keywords: Shell

Variables

Variables from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/03-var.md.

Keywords: Shell

Loops

Loops from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/04-loop.md.

Keywords: Shell

Creating Things

Creating Things from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/02-create.md.

Keywords: Shell

Shell Scripts

Shell Scripts from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/05-script.md.

Keywords: Shell

Pipes and Filters

Pipes and Filters from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/03-pipefilter.md.

Keywords: Shell

Introducing the Shell

Introducing the Shell from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/00-intro.md.

Keywords: Shell

Finding Things

Finding Things from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/06-find.md.

Keywords: Shell

Files and Directories

Files and Directories from https://github.com/swcarpentry/bc/tree/gh-pages/novice/shell/01-filedir.md.

Keywords: Shell

Permissions

Permissions from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/01-perm.md.

Keywords: Shell

Working Remotely

Working Remotely from https://github.com/swcarpentry/bc/tree/gh-pages/intermediate/shell/02-ssh.md.

Keywords: Shell