Code Monkey home page Code Monkey logo

biotea-box's Introduction

BioTEA-box

This repository hosts the code for the BioTEA Docker container. The container runs the analysis itself.

The BioTEA repo contains the guides and extra information on the tool. Click here to go to it

Installation

You do not need to install BioTEA-Box locally. BioTEA takes care of that for you. Please check that repository instead.

Issues

Have an issue with the box? File a new issue! Be as detailed as you can so we can solve the issue quickly. Also check out bioTEA's issues: your problem may have already been submitted.

Have a question about BioTEA? Send an issue in the main repository.

Contributing

Check the CONTRIBUTING.md file if you want to contribute.

biotea-box's People

Contributors

feat-fear avatar mrhedmad avatar

biotea-box's Issues

Restructure Annotation Procedure

This issue was raised by @Feat-FeAR :

The internal annotations for human chips do not have linked scripts for re-generation. Additionally, there are other considerations to make:

  • Many Agilent microarrays do not have annotations as bioconductor packages, but only as GEO GPL accessions. This should be addressed by adding annotations for all Agilent arrays.
  • The annotated columns as gene symbols should be surpassed by ENSG when possible. This has all the benefits of using ENSGs instead of gene names, plus it better supports RNA-Seq, which by default is annotated with ENSGs in most pipelines.

Generalize expression matrix first column name

Currently, the name of the first column of the expression matrix loaded by read_expression_data() is hard-coded to be "probe_id"... this is fragile and conceptually incorrect for a probe-independent technology like RNA-Seq. We should remove such a constraint.

Recommend Projects

  • React photo React

    A declarative, efficient, and flexible JavaScript library for building user interfaces.

  • Vue.js photo Vue.js

    🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.

  • Typescript photo Typescript

    TypeScript is a superset of JavaScript that compiles to clean JavaScript output.

  • TensorFlow photo TensorFlow

    An Open Source Machine Learning Framework for Everyone

  • Django photo Django

    The Web framework for perfectionists with deadlines.

  • D3 photo D3

    Bring data to life with SVG, Canvas and HTML. 📊📈🎉

Recommend Topics

  • javascript

    JavaScript (JS) is a lightweight interpreted programming language with first-class functions.

  • web

    Some thing interesting about web. New door for the world.

  • server

    A server is a program made to process requests and deliver data to clients.

  • Machine learning

    Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.

  • Game

    Some thing interesting about game, make everyone happy.

Recommend Org

  • Facebook photo Facebook

    We are working to build community through open source technology. NB: members must have two-factor auth.

  • Microsoft photo Microsoft

    Open source projects and samples from Microsoft.

  • Google photo Google

    Google ❤️ Open Source for everyone.

  • D3 photo D3

    Data-Driven Documents codes.