eggduzao
Affiliated Professor / Computational Biologist / Some repositories are simply the code and data for a particular project or manuscript.
Technische Universität München (TUM)Germany, Brazil
Pinned Repositories
Casa_et_al
Source code for all analysis performed in the publication by Casa et al. "Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcriptional control"
Gothe_et_al
Source scripts used for bioinformatic analyses of the paper by Goethe et al. "Spatial chromosome folding and active transcription drive DNA fragility and formation of oncogenic MLL translocations"
reg-gen
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
4DN-AWS-pipeline
Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.
Bloom
Bloom: A computational framework to reveal occult patterns in 3C contact maps
Costa_Dream
ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge
Gusmao_RGT
REDCap-PRO
REDCapPRO is an external module for REDCap that enables Patient Reported Outcomes in a manner that complies with regulatory stipulations.
4DN-docker-hic
Docker for 4DN Hi-C processing pipeline
4DN-pipelines-cwl
Pipelines developed and used by 4DN-DCIC in Common Workflow Language
eggduzao's Repositories
eggduzao/Stainalyzer
Open and publicly available tool to automatically evaluate immunohistochemically-stained antibodies
eggduzao/biolearn
Machine learning tools for biomarker analysis and standardization
eggduzao/REDCap-Vizr
A REDCap external module to visualize project data over time.
eggduzao/REDCap-instance-table
Use the action tag @INSTANCETABLE=form_name in a descriptive text field to include a table showing data from repeat instances of that form. If project is longitudinal, use @INSTANCETABLE=event_name:form_name to specify the event and form (can be a repeating form or a form in a repeating event).
eggduzao/REDCap-PRO
REDCapPRO is an external module for REDCap that enables Patient Reported Outcomes in a manner that complies with regulatory stipulations.
eggduzao/4DN-AWS-pipeline
Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.
eggduzao/REDCap-autofill
A REDCap external module providing action tags that allow filling of empty fields with default values
eggduzao/4DN-docker-hic
Docker for 4DN Hi-C processing pipeline
eggduzao/ENCODE-atac-seq-pipeline
ENCODE ATAC-seq pipeline
eggduzao/4DN-pipelines-cwl
Pipelines developed and used by 4DN-DCIC in Common Workflow Language
eggduzao/REDCap-pdf-injector
PDF Injector is a REDCap module that enables you to populate fillable PDFs with record data from variables.
eggduzao/ENCODE-hic-pipeline
HiC uniform processing pipeline
eggduzao/ENCODE-regulome-encoded
Temp repo for regulome development
eggduzao/SingleCellRnaSeq
eggduzao/ENCODE-correlation_robustness
eggduzao/Gothe_et_al
Source scripts used for bioinformatic analyses of the paper by Goethe et al. "Spatial chromosome folding and active transcription drive DNA fragility and formation of oncogenic MLL translocations"
eggduzao/GATK4-data-processing
Workflows for processing high-throughput sequencing data for variant discovery with GATK4 and related tools
eggduzao/WGS-QC-Pipeline
A Snakemake pipeline for Quality Control of Whole Genome Sequencing data
eggduzao/Bloom
Bloom: A computational framework to reveal occult patterns in 3C contact maps
eggduzao/GATK4-germline-snps-indels
Workflows for germline short variant discovery with GATK4
eggduzao/ENCODE-long-rna-seq-pipeline
STAR based ENCODE Long RNA-Seq processing pipeline
eggduzao/GATK4-genome-processing-pipeline
Workflows used for processing whole genome sequence data + germline variant calling. This Repository has been archived, please visit the link the ReadMe to obtain the latest version of the workflow.
eggduzao/ENCODE-chip-seq-pipeline
ENCODE Uniform processing pipeline for ChIP-seq
eggduzao/Casa_et_al
Source code for all analysis performed in the publication by Casa et al. "Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcriptional control"
eggduzao/Zenke_DendriticCells
eggduzao/Wagner_StemAging
eggduzao/Wagner_Methylation
eggduzao/Tenbrock_Tlf4Erythroid
eggduzao/Souto_NegativeSampling
eggduzao/Rosengren_TIID