wirawara

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/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