Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
Projects in Awesome Lists by jorainer
A curated list of projects in awesome lists by jorainer .
https://github.com/jorainer/ensembldb
This is the ensembldb development repository.
annotation bioconductor bioconductor-packages ensembl
Last synced: 01 Nov 2024
https://github.com/jorainer/metabolomics2018
Workshop illustrating mass spectrometry data analysis in R and use of the updated xcms functionality for the preprocessing of LC-MS data.
Last synced: 12 Oct 2024
https://github.com/jorainer/spectratutorials
These workshops and tutorials provide use cases and examples for mass spectrometry data handling and analysis using the Spectra Bioconductor package.
Last synced: 12 Oct 2024
https://github.com/jorainer/atc
This package provides the Anatomical Therapeutical Chemical (ATC) Classification data from WHOCC and implements functions that facilitate working with these.
Last synced: 12 Oct 2024
https://github.com/jorainer/metaboannotationtutorials
Examples and tutorials for the MetaboAnnotation, MetaboCoreUtils and CompoundDb R packages
annotation mass-spectrometry metabolomics
Last synced: 12 Oct 2024
https://github.com/jorainer/xcmstutorials
Tutorials and workshops describing LC-MS(/MS) data pre-processing and analysis using the xcms Bioconductor package
Last synced: 12 Oct 2024
https://github.com/jorainer/xcms-gnps-tools
Utility functions for the use of xcms with GNPS
Last synced: 12 Oct 2024
https://github.com/jorainer/bioc2016-ensembldb
Presentation for the BioC 2016 conference in Stanford
Last synced: 12 Oct 2024
https://github.com/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.
Last synced: 12 Oct 2024
https://github.com/jorainer/spectra_workshop
Workshop about the RforMassSpectrometry Spectra R package.
Last synced: 12 Oct 2024
https://github.com/jorainer/metabolomics2023
Contribution to the Metabolomics 2023 conference of the Metabolomics Society
Last synced: 12 Oct 2024
https://github.com/jorainer/swemsa_2019
Talk for the SWEMSA 2019 conference/workshop
Last synced: 12 Oct 2024
https://github.com/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.
Last synced: 12 Oct 2024
https://github.com/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
Last synced: 12 Oct 2024
https://github.com/jorainer/eurobioc2024
Contribution to the EuroBioC2024 conference
Last synced: 12 Oct 2024
https://github.com/jorainer/xcmsextensions
Collection of methods and functions extending the functionality of the xcms Bioconductor package.
Last synced: 12 Oct 2024
https://github.com/jorainer/compounddb.hsapiens.hmdb.4.0
HMDB (http://www.hmdb.ca) compound database for PeakABro (https://github.com/stanstrup/PeakABro)
Last synced: 12 Oct 2024
https://github.com/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.
Last synced: 12 Oct 2024
https://github.com/jorainer/ensembl-exon-probemapping
Perl scripts to create custom CDF files and packages for Affymetrix microarrays.
Last synced: 12 Oct 2024
https://github.com/jorainer/timealarms
Slightly modified of the TimeAlarms arduino library (http://www.pjrc.com/teensy/td_libs_TimeAlarms.html).
Last synced: 12 Oct 2024
https://github.com/jorainer/ahensdbs
Supplies AnnotationHub with EnsDb Ensembl-based annotation databases for all species.
Last synced: 12 Oct 2024
https://github.com/jorainer/mirtarbase-db
R package providing the validate miRNA-target gene interactions (MTIs) from the miRTarBase database.
Last synced: 12 Oct 2024
https://github.com/jorainer/mirtarbase
mirtarbase: a database of validated miRNA target gene interactions, as provided by the miRTarBase (http://mirtarbase.mbc.nctu.edu.tw/)
Last synced: 12 Oct 2024
https://github.com/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.
Last synced: 12 Oct 2024
https://github.com/jorainer/install_scripts
Some installation scripts to easily set up Mac OS system to my needs.
Last synced: 12 Oct 2024
https://github.com/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.
Last synced: 12 Oct 2024
https://github.com/jorainer/mirhostdb.hsapiens.v75.v20
Definition of miRNA host genes based on Ensembl version 75 and miRBase version 20.
Last synced: 12 Oct 2024
https://github.com/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.
Last synced: 12 Oct 2024
https://github.com/jorainer/mirhostgenes
mirhostgenes: putting miRNAs into genomic context. Definitions of potential primary transcription units for miRNAs and microarray probe sets that would allow to detect/measure these.
Last synced: 12 Oct 2024
https://github.com/jorainer/jos-csama-contributions
Lectures and labs I'm providing/giving at the CSAMA Bioconductor courses
Last synced: 12 Oct 2024
https://github.com/jorainer/eurobioc2016-ensembldb
Material for the European Bioconductor Developer's Meeting 2016 in Basel, Switzerland
Last synced: 12 Oct 2024
https://github.com/jorainer/gruvbox-emacs
Simple Emacs color theme based on the gruvbox theme for Vim and using logic from the solarized-emacs theme.
Last synced: 12 Oct 2024
https://github.com/jorainer/metabolomics2020
Contribution to the (online) conference from the metabolomics society metabolomics2020 (http://metabolomics2020.org/)
Last synced: 12 Oct 2024
https://github.com/jorainer/enhancedtxdbs
Provides functions for creating Bioconductor TranscriptDb objects from Ensembl.
Last synced: 12 Oct 2024
https://github.com/jorainer/memacs
Make file to fetch and build emacs add-ons.
Last synced: 12 Oct 2024
https://github.com/jorainer/clydeclock
Enables clock functionality for Clyde (http://www.fabule.com/).
Last synced: 12 Oct 2024
https://github.com/jorainer/rnw-based-affy-analysis
Standard analysis of Affymetrix microarrays defined using Rnw files.
Last synced: 12 Oct 2024
https://github.com/jorainer/sequtils
R package provides some utility functions for the processing of sequencing data which complement the functionality of other packages handling such data.
Last synced: 12 Oct 2024
https://github.com/jorainer/generalgcrma
An R package to perform GCRMA background adjustment for Affymetrix Tiling, Exon and Gene ST microarrays.
Last synced: 12 Oct 2024
https://github.com/jorainer/annotation_ecosystem
Supplementary material for the annotation ecosystem paper.
Last synced: 12 Oct 2024
https://github.com/jorainer/eurobioc2017-annotationfilter
Slides for flashlight talk for AnnotationFilter and ensembldb at the European Bioconductor Meeting 2017 in Cambridge, UK.
Last synced: 12 Oct 2024
https://github.com/jorainer/eurobioc2018-ensembldb
Slides for the European Bioconductor developer conference 2018
Last synced: 12 Oct 2024
https://github.com/jorainer/flatui-emacs
Emacs theme based on the Falt UI color scheme
Last synced: 12 Oct 2024
https://github.com/jorainer/metaboannotationintro
Introductions and tutorials/presentations for the MetaboAnnotation package
Last synced: 12 Oct 2024
https://github.com/jorainer/csama
Lectures and workshops for the CSAMA Bioconductor workshop
Last synced: 12 Oct 2024