Workflows
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Workflow type
Python1
Tag
Bioinformatics1
gene expression correlation1
gene expression data wrangling1
geo database mining1
Submitter
Yasmmin Martins1
Space
Independent Teams1
Topic annotations
Expression correlation analysis1
Operation annotations
Expression correlation analysis1
Variant calling6
Annotation5
Sequencing quality control5
Sequence assembly4
Data retrieval3
Gene-set enrichment analysis3
Protein interaction network analysis3
Variant classification3
Variant filtering3
Conversion2
Correlation2
Gene functional annotation2
Genome annotation2
Haplotype mapping2
Modelling and simulation2
Prediction and recognition2
Protein interaction network prediction2
SNP annotation2
Weighted correlation network analysis2
Analysis1
Antimicrobial resistance prediction1
Binding site prediction1
Calculation1
Classification1
Clustering1
Contact map calculation1
Copy number variation detection1
Data handling1
Differential gene expression profiling1
Dimensionality reduction1
DNA barcoding1
Enrichment analysis1
Feature extraction1
Format detection1
Genome assembly1
ID mapping1
Image analysis1
k-mer counting1
Metabolic pathway prediction1
Named-entity and concept recognition1
Network analysis1
Nucleic acid property calculation1
Peptide identification1
Phylogenetic inference1
Protein identification1
Protein-protein interaction analysis1
Read mapping1
Relation extraction1
RNA-Seq analysis1
Sequence alignment analysis (site correlation)1
Sequence annotation1
Sequence contamination filtering1
Sequence distance matrix generation1
Sequence profile generation1
Single particle analysis1
Standardisation and normalisation1
Taxonomic classification1
Text annotation1
Text mining1
Transcription factor binding site prediction1
More...
Maturity
Stable1
1
Workflow matching the given criteria:
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Operation annotations:
Expression correlation analysis1
Stable
Summary
The PPI information aggregation pipeline starts getting all the datasets in GEO database whose material was generated using expression profiling by high throughput sequencing. From each database identifiers, it extracts the supplementary files that had the counts table. Once finishing the download step, it identifies those that were normalized or had the raw counts to normalize. It also identify and map the gene ids to uniprot (the ids found usually ...
