jorainer/AHEnsDbs

Supplies AnnotationHub with EnsDb Ensembl-based annotation databases for all species.

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jorainer/SpectraTutorials

These workshops and tutorials provide use cases and examples for mass spectrometry data handling and analysis using the Spectra Bioconductor package.

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jorainer/xcmsTutorials

Tutorials and workshops describing LC-MS(/MS) data pre-processing and analysis using the xcms Bioconductor package

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jorainer/AnnotationDbi Fork of jimhester/AnnotationDbi

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/AnnotationDbi.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=AnnotationDbi.

Language: R - Size: 5.17 MB - Last synced: 17 days ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0

jorainer/auroracoin-project Fork of baldurodinsson/auroracoin-project

Language: TypeScript - Size: 2.15 MB - Last synced: 17 days ago - Pushed: over 10 years ago - Stars: 0 - Forks: 0

jorainer/Clyde Fork of fabule/Clyde

Clyde is an open source Arduino-compatible lamp with a lot of personality that you can adapt, play with, and truly call your own.

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jorainer/annotation_ecosystem

Supplementary material for the annotation ecosystem paper.

Language: TeX - Size: 5.21 MB - Last synced: 17 days ago - Pushed: over 2 years ago - Stars: 0 - Forks: 0

jorainer/emacs-leuven-theme Fork of fniessen/emacs-leuven-theme

Awesome Emacs color theme for white backgrounds --- Added in Emacs 24.4

Language: Emacs Lisp - Size: 923 KB - Last synced: 17 days ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0

jorainer/CSAMA_website Fork of Huber-group-EMBL/CSAMA_website

Website for CSAMA

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jorainer/MirhostDb.Hsapiens.v75.v20

Definition of miRNA host genes based on Ensembl version 75 and miRBase version 20.

Language: R - Size: 2.09 MB - Last synced: 17 days ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0

jorainer/MSEntropy Fork of YuanyueLi/MSEntropy

Spectral entropy for mass spectrometry data.

Language: Python - Size: 377 KB - Last synced: 17 days ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

jorainer/pwiz Fork of ProteoWizard/pwiz

The ProteoWizard Library is a set of software libraries and tools for rapid development of mass spectrometry and proteomic data analysis software.

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jorainer/Spectra Fork of AharoniLab/Spectra

Low level infrastructure to handle MS spectra

Language: R - Size: 2.11 MB - Last synced: 17 days ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

jorainer/org-mode-notes

Some notes on how to use org-mode for literature programming and enable export of org files to Rmd format to be used with rmarkdown.

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jorainer/RaMP-DB Fork of ncats/RaMP-DB

Size: 1.3 GB - Last synced: 17 days ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

jorainer/solarized-emacs Fork of bbatsov/solarized-emacs

The Solarized colour theme, ported to Emacs.

Language: Emacs Lisp - Size: 868 KB - Last synced: 17 days ago - Pushed: over 8 years ago - Stars: 0 - Forks: 0

jorainer/SeqUtils

R package provides some utility functions for the processing of sequencing data which complement the functionality of other packages handling such data.

Language: R - Size: 2.48 MB - Last synced: 17 days ago - Pushed: almost 9 years ago - Stars: 0 - Forks: 0

jorainer/generalgcrma

An R package to perform GCRMA background adjustment for Affymetrix Tiling, Exon and Gene ST microarrays.

Language: R - Size: 188 KB - Last synced: 17 days ago - Pushed: over 9 years ago - Stars: 0 - Forks: 0

jorainer/Gviz

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/Gviz.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=Gviz.

Language: R - Size: 3.75 MB - Last synced: 17 days ago - Pushed: over 8 years ago - Stars: 3 - Forks: 5

jorainer/ensembldb-old

NOTE: that's the version prior to the Bioconductor github mirror. The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, the ensembldb package provides also a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes.

Language: R - Size: 777 KB - Last synced: 17 days ago - Pushed: almost 9 years ago - Stars: 0 - Forks: 0

jorainer/mirtarbase-db

R package providing the validate miRNA-target gene interactions (MTIs) from the miRTarBase database.

Language: R - Size: 5.43 MB - Last synced: 17 days ago - Pushed: almost 10 years ago - Stars: 1 - Forks: 2

jorainer/bioconductor.org Fork of Bioconductor/bioconductor.org

Source code for the Bioconductor website

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jorainer/EuroBioC2024

Contribution to the EuroBioC2024 conference

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jorainer/metabolomics2023

Contribution to the Metabolomics 2023 conference of the Metabolomics Society

Size: 37.1 KB - Last synced: 17 days ago - Pushed: about 1 year ago - Stars: 2 - Forks: 11

jorainer/MetaboAnnotationTutorials

Examples and tutorials for the MetaboAnnotation, MetaboCoreUtils and CompoundDb R packages

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jorainer/metabolomics2018

Workshop illustrating mass spectrometry data analysis in R and use of the updated xcms functionality for the preprocessing of LC-MS data.

Language: HTML - Size: 22.3 MB - Last synced: 17 days ago - Pushed: about 1 year ago - Stars: 25 - Forks: 12

jorainer/MsBackendRawFileReader Fork of fgcz/MsBackendRawFileReader

Spectra MsBackend for Thermo Fisher Scientific's New RawFileReader

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jorainer/atc

This package provides the Anatomical Therapeutical Chemical (ATC) Classification data from WHOCC and implements functions that facilitate working with these.

Language: R - Size: 5.76 MB - Last synced: 17 days ago - Pushed: almost 2 years ago - Stars: 15 - Forks: 3

jorainer/ensembldb

This is the ensembldb development repository.

Language: R - Size: 6.57 MB - Last synced: 23 days ago - Pushed: about 2 months ago - Stars: 33 - Forks: 10

jorainer/MetaboAnnotation Fork of AharoniLab/MetaboAnnotation

High level functionality to support and simplify metabolomics data annotation.

Language: R - Size: 1.23 MB - Last synced: 17 days ago - Pushed: 10 months ago - Stars: 0 - Forks: 0

jorainer/psi-ms-CV Fork of HUPO-PSI/psi-ms-CV

HUPO-PSI mass spectrometry CV

Language: Python - Size: 5.96 MB - Last synced: 17 days ago - Pushed: 11 months ago - Stars: 0 - Forks: 0

jorainer/AHMassBank

MassBank metadata for AnnotationHub

Language: R - Size: 13.7 KB - Last synced: 9 days ago - Pushed: 6 months ago - Stars: 1 - Forks: 0

jorainer/MsQuality_manuscript Fork of tnaake/MsQuality_manuscript

Language: TeX - Size: 2.57 MB - Last synced: 17 days ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

jorainer/xcms-gnps-tools

Utility functions for the use of xcms with GNPS

Language: R - Size: 11.7 KB - Last synced: 17 days ago - Pushed: over 4 years ago - Stars: 5 - Forks: 3

jorainer/chadwm Fork of siduck/chadwm

Making dwm as beautiful as possible!

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jorainer/CSAMA

Lectures and workshops for the CSAMA Bioconductor workshop

Size: 28.2 MB - Last synced: 17 days ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

jorainer/memacs

Make file to fetch and build emacs add-ons.

Language: Emacs Lisp - Size: 1.63 MB - Last synced: 17 days ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

jorainer/mzR Fork of sneumann/mzR

This is the git repository matching the Bioconductor package mzR: parser for netCDF, mzXML, mzData and mzML files (mass spectrometry data)

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jorainer/BiocWorkingGroups Fork of Bioconductor/BiocWorkingGroups

Bioconductor working group guidelines. Also, a list of active, suggested, and inactive working groups for bioconductor for the community to volunteer to be apart of. The community is also welcome to suggest new working groups.

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jorainer/cpc Fork of krispir/cpc

The purpose of the cpc package is primarily to characterize the peaks detected using a separate peak detection method. Currently the only supported preprocessing software is XCMS.

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jorainer/biocblog Fork of Bioconductor/biocblog

A Distill Blog for Bioconductor community

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jorainer/XCMS3_FeatureBasedMN Fork of DorresteinLaboratory/XCMS3_FeatureBasedMN

Language: Jupyter Notebook - Size: 801 KB - Last synced: 17 days ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

jorainer/MetaboAnnotationIntro

Introductions and tutorials/presentations for the MetaboAnnotation package

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jorainer/CodeOfConduct Fork of Bioconductor/CodeOfConduct

Size: 2.33 MB - Last synced: 17 days ago - Pushed: about 2 years ago - Stars: 0 - Forks: 0

jorainer/install_scripts

Some installation scripts to easily set up Mac OS system to my needs.

Language: Shell - Size: 220 KB - Last synced: 17 days ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

jorainer/pkgrevdocs Fork of Bioconductor/pkgrevdocs

Training Material for Community Reviewers

Language: R - Size: 970 KB - Last synced: 17 days ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

jorainer/Bioconductor20YearsSlides Fork of kevinrue/Bioconductor20YearsSlides

Carousel of xaringan slides to celebrate 20 years of the Bioconductor project.

Language: R - Size: 147 MB - Last synced: 17 days ago - Pushed: almost 3 years ago - Stars: 0 - Forks: 0

jorainer/ProtGenerics Fork of rformassspectrometry/ProtGenerics

S4 generic functions for Bioconductor proteomics infrastructure

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jorainer/bioc_package_guide Fork of kozo2/bioc_package_guide

Guidelines for Bioconductor package development and review

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jorainer/testrepo

tiny test repo

Language: R - Size: 2.93 KB - Last synced: 17 days ago - Pushed: about 3 years ago - Stars: 0 - Forks: 0

jorainer/MsBackendMassbank Fork of rformassspectrometry/MsBackendMassbank

A prototype backend to parse MassBank records into Spectra

Language: R - Size: 320 KB - Last synced: 17 days ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

jorainer/S4Vectors Fork of Bioconductor/S4Vectors

Foundation of vector-like and list-like containers in Bioconductor

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jorainer/ChIPseeker Fork of YuLab-SMU/ChIPseeker

:dart:ChIP peak Annotation, Comparison and Visualization

Language: R - Size: 17.2 MB - Last synced: 17 days ago - Pushed: over 3 years ago - Stars: 0 - Forks: 1

jorainer/EnsDb.Hsapiens.v75

EnsDb database containing Ensembl based human gene/transcript annotations for Ensembl version 75. This repository represents the developmental version of the official package from Bioconductor http://www.bioconductor.org/packages/EnsDb.Hsapiens.v75

Language: R - Size: 2.93 KB - Last synced: 17 days ago - Pushed: over 7 years ago - Stars: 1 - Forks: 0

jorainer/BiocChallenges Fork of kevinrue/BiocChallenges

Challenges for the Biocoductor community.

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jorainer/MassBank-web Fork of MassBank/MassBank-web

The web server application and directly connected components for a MassBank web server

Size: 60.3 MB - Last synced: 17 days ago - Pushed: over 3 years ago - Stars: 0 - Forks: 0

jorainer/metabolomics2020

Contribution to the (online) conference from the metabolomics society metabolomics2020 (http://metabolomics2020.org/)

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jorainer/MetCirc Fork of tnaake/MetCirc

GitHub repository for MetCirc. The development version in Bioconductor can be found at:

Language: R - Size: 5.43 MB - Last synced: 17 days ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

jorainer/spectra_workshop

Workshop about the RforMassSpectrometry Spectra R package.

Language: HTML - Size: 43.9 MB - Last synced: 17 days ago - Pushed: over 4 years ago - Stars: 2 - Forks: 1

jorainer/GSEABase Fork of Bioconductor/GSEABase

Gene set enrichment data structures and methods

Size: 327 KB - Last synced: 17 days ago - Pushed: about 4 years ago - Stars: 0 - Forks: 0

jorainer/Pbase Fork of lgatto/Pbase

Manipluating and exploring protein and proteomics data

Language: R - Size: 22.5 MB - Last synced: 17 days ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

jorainer/SQLDataFrame Fork of Bioconductor/SQLDataFrame

DataFrame representation of SQL database table

Size: 390 KB - Last synced: 17 days ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

jorainer/xcmsExtensions

Collection of methods and functions extending the functionality of the xcms Bioconductor package.

Language: R - Size: 6.01 MB - Last synced: 17 days ago - Pushed: about 8 years ago - Stars: 1 - Forks: 0

jorainer/CAMERA Fork of sneumann/CAMERA

This is the git repository matching the Bioconductor package CAMERA: Collection of annotation related methods for mass spectrometry data

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jorainer/bioconductor-vignettes Fork of elixir-metabolomics-community/bioconductor-vignettes

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jorainer/iSEE_gviz Fork of plger/iSEE_gviz

custom gviz panel for iSEE

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jorainer/swemsa_2019

Talk for the SWEMSA 2019 conference/workshop

Language: HTML - Size: 60.8 MB - Last synced: 17 days ago - Pushed: over 4 years ago - Stars: 2 - Forks: 1

jorainer/GNPSDocumentation Fork of lfnothias/GNPSDocumentation

Language: Python - Size: 98.3 MB - Last synced: 17 days ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

jorainer/wiggleplotr Fork of kauralasoo/wiggleplotr

A small R package to make sequencing read coverage plots in R.

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jorainer/github-example

Just some test repository

Size: 2.93 KB - Last synced: 17 days ago - Pushed: over 4 years ago - Stars: 0 - Forks: 0

jorainer/unsoRted

Unsorted R functions and utilities.

Language: R - Size: 35.2 KB - Last synced: 17 days ago - Pushed: over 8 years ago - Stars: 1 - Forks: 0

jorainer/test_analysis

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jorainer/MSnio Fork of meowcat/MSnio

Language: R - Size: 51.8 KB - Last synced: 17 days ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

jorainer/CompoundDb.Hsapiens.HMDB.4.0

HMDB (http://www.hmdb.ca) compound database for PeakABro (https://github.com/stanstrup/PeakABro)

Language: R - Size: 5.21 MB - Last synced: 17 days ago - Pushed: over 6 years ago - Stars: 1 - Forks: 1

jorainer/MSnbase Fork of meowcat/MSnbase

Base Classes and Functions for Mass Spectrometry and Proteomics

Language: R - Size: 37.6 MB - Last synced: 17 days ago - Pushed: about 5 years ago - Stars: 0 - Forks: 0

jorainer/PeakABro Fork of stanstrup/PeakABro

Peaklist Annotator and Browser

Language: R - Size: 120 KB - Last synced: 17 days ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

jorainer/gruvbox-emacs

Simple Emacs color theme based on the gruvbox theme for Vim and using logic from the solarized-emacs theme.

Language: Emacs Lisp - Size: 36.1 KB - Last synced: 17 days ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

jorainer/flatui-emacs

Emacs theme based on the Falt UI color scheme

Language: Emacs Lisp - Size: 68.4 KB - Last synced: 17 days ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

jorainer/rnaseqGene Fork of thelovelab/rnaseqGene

RNA-seq workflow: gene-level exploratory analysis and differential expression

Size: 142 KB - Last synced: 17 days ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

jorainer/GenomeInfoDb Fork of Bioconductor/GenomeInfoDb

Utilities for manipulating chromosome and other 'seqname' identifiers

Language: R - Size: 82.3 MB - Last synced: 17 days ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

jorainer/EuroBioc2018-ensembldb

Slides for the European Bioconductor developer conference 2018

Language: CSS - Size: 261 KB - Last synced: 17 days ago - Pushed: over 5 years ago - Stars: 0 - Forks: 1

jorainer/github_playground

Some testing stuff

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jorainer/cdkr Fork of CDK-R/cdkr

Integrating R and the CDK

Language: R - Size: 269 MB - Last synced: 17 days ago - Pushed: over 6 years ago - Stars: 0 - Forks: 0

jorainer/emacs-theme-creamsody Fork of emacsfodder/emacs-theme-creamsody

An Emacs color theme, Straight from the soda fountain.

Language: Emacs Lisp - Size: 9.51 MB - Last synced: 17 days ago - Pushed: over 5 years ago - Stars: 0 - Forks: 0

jorainer/biovizBase

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/biovizBase.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=biovizBase.

Language: R - Size: 3.64 MB - Last synced: 17 days ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 2

jorainer/MetaboAnalystR Fork of xia-lab/MetaboAnalystR

R package for MetaboAnalyst

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jorainer/jotsetung.github.io

some html content.

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jorainer/jos-csama-contributions

Lectures and labs I'm providing/giving at the CSAMA Bioconductor courses

Size: 22.7 MB - Last synced: 17 days ago - Pushed: almost 6 years ago - Stars: 0 - Forks: 0

jorainer/macbook-keyboard-fix.el

Simple emacs mode that avoids double/triple insertion of certain characters from a single key stroke happening on the new butterfly keyboard on macbook pro > 2016.

Language: Emacs Lisp - Size: 1.95 KB - Last synced: 17 days ago - Pushed: about 6 years ago - Stars: 0 - Forks: 0

jorainer/EuroBioc2017-MSnbase

Slides for the flashlight talk about on-the-fly data access and MS write support added to mzR/MSnbase/xcms for the European Bioconductor Developer Meeting 2017 in Cambridge, UK.

Language: TeX - Size: 737 KB - Last synced: 17 days ago - Pushed: over 6 years ago - Stars: 1 - Forks: 0

jorainer/EuroBioc2017-AnnotationFilter

Slides for flashlight talk for AnnotationFilter and ensembldb at the European Bioconductor Meeting 2017 in Cambridge, UK.

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jorainer/rcdk Fork of cran/rcdk

:exclamation: This is a read-only mirror of the CRAN R package repository. rcdk — Interface to the 'CDK' Libraries

Language: R - Size: 21.6 MB - Last synced: 17 days ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0

jorainer/Ensembl-Exon-probemapping

Perl scripts to create custom CDF files and packages for Affymetrix microarrays.

Language: Perl - Size: 258 KB - Last synced: 17 days ago - Pushed: about 8 years ago - Stars: 1 - Forks: 0

jorainer/dummy_test

Language: R - Size: 0 Bytes - Last synced: 17 days ago - Pushed: almost 7 years ago - Stars: 0 - Forks: 0

jorainer/TimeAlarms

Slightly modified of the TimeAlarms arduino library (http://www.pjrc.com/teensy/td_libs_TimeAlarms.html).

Language: C++ - Size: 121 KB - Last synced: 17 days ago - Pushed: over 9 years ago - Stars: 1 - Forks: 1

jorainer/ggbio Fork of knapier/ggbio

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/ggbio.html Contributions: http://tengfei.github.com/ggbio/. Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=ggbio or https://github.com/tengfei/ggbio/issues.

Language: R - Size: 2.3 MB - Last synced: 17 days ago - Pushed: about 7 years ago - Stars: 0 - Forks: 0

jorainer/Organism.dplyr Fork of Bioconductor/Organism.dplyr

Language: R - Size: 790 KB - Last synced: 17 days ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

jorainer/EuroBioC2016-ensembldb

Material for the European Bioconductor Developer's Meeting 2016 in Basel, Switzerland

Language: R - Size: 313 KB - Last synced: 17 days ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

jorainer/Fill-Column-Indicator Fork of alpaker/fill-column-indicator

An Emacs minor mode that graphically indicates the fill column.

Language: Emacs Lisp - Size: 252 KB - Last synced: 17 days ago - Pushed: over 7 years ago - Stars: 0 - Forks: 0

jorainer/EuroBioc2016-Basel-MSnbase2 Fork of lgatto/2016_12_6_EuroBioc_Basel

Slides for the EuroBioc2016 meeting in Basel

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