wirawara
Ph.D. in Bioinformatics / Systems Biology - Zürich/Lausanne. Cornell. #1 in Bioinformatics. Single-cell, multi-omics. 📍Vienna
@sib-swiss @BgeeDB ETH/University of Zurich, Switzerland
Pinned Repositories
Basset
Convolutional neural network analysis for predicting DNA sequence activity.
BgeeDB
an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests, Komljenovic et al. f1000Research
BiocAdvanced
Advanced R / Bioconductor training material
Bioinfo_Pipelines
Pipelines for RNAseq, Chipseq, ...
chip-seq-pipeline2
ENCODE ChIP-seq pipeline
Cross_species_integration
Code to analyze cross-species functional modules link proteostasis to human normal aging, Komljenovic et al. Plos Comp Bio
Lifespan-paper-collaboration
code to analyze RNA-seq and microarrays, for lifespan paper
Oncogenesis-paper-
Code to analyze Epigenetic silencing of monoallelically methylated miRNA loci in precancerous colorectal lesions.
targetedmetabolomics_paper
Code to analyze targeted metabolomics, RNAseq, scRNAseq and other miscellaneous in vitro metabolomics data
wirawara.github.io
Andrea's github pages
wirawara's Repositories
wirawara/BgeeDB
an R package for retrieval of curated expression datasets and for gene list expression localization enrichment tests, Komljenovic et al. f1000Research
wirawara/targetedmetabolomics_paper
Code to analyze targeted metabolomics, RNAseq, scRNAseq and other miscellaneous in vitro metabolomics data
wirawara/wirawara.github.io
Andrea's github pages
wirawara/Basset
Convolutional neural network analysis for predicting DNA sequence activity.
wirawara/BiocAdvanced
Advanced R / Bioconductor training material
wirawara/Bioinfo_Pipelines
Pipelines for RNAseq, Chipseq, ...
wirawara/chip-seq-pipeline2
ENCODE ChIP-seq pipeline
wirawara/Cross_species_integration
Code to analyze cross-species functional modules link proteostasis to human normal aging, Komljenovic et al. Plos Comp Bio
wirawara/Lifespan-paper-collaboration
code to analyze RNA-seq and microarrays, for lifespan paper
wirawara/cromwell
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
wirawara/EpigenomicsTutorial-ISMB2017
Repository for the Epigenomics Tutorial hold at ISMB 2017 in Prague
wirawara/feather
Feather: fast, interoperable binary data frame storage for Python, R, and more powered by Apache Arrow
wirawara/Giotto
Spatial omics analysis toolbox
wirawara/Gviz_visualizations
Collection of the scripts for the integrative sequencing visualizations
wirawara/GWAS-stats-genetics
resources when working with GWAS summary stats
wirawara/itaconate_paper
Code to analyze human samples
wirawara/miloR
R package implementation of Milo for testing for differential abundance in KNN graphs
wirawara/ogb
Benchmark datasets, data loaders, and evaluators for graph machine learning
wirawara/omicsplayground
Visual self-service analytics platform for big omics data.
wirawara/phd_thesis_markdown
Template for writing a PhD thesis in Markdown
wirawara/python-machine-learning-book
The "Python Machine Learning" book code repository and info resource
wirawara/regression_survival_analysis_R
collection of the R scripts for the clinical datasets
wirawara/remake
Make-like declarative workflows in R
wirawara/scQC
an R package; a method for multivariate QC for large-scale single-cell RNA-seq datasets.
wirawara/Spatial_ATAC-seq
wirawara/SpatialBook
Book on Spatial Omics Analysis with Bioconductor
wirawara/spatialdata
An open and universal framework for processing spatial omics data
wirawara/SpatialExperiment
wirawara/starting_with_docker
docker pipelines
wirawara/versatile-genomics-scripts