I am commited to open and reproducible science.
Released tools
- Corre, a DNA co-methylation browser in colon cancer (Miguel A. Peinado's lab, 2017).
- Pan-cancer DNA methylation trackhub, a DNA methylation layer to the Genome Browser (Miguel A. Peinado's lab, 2017). Source.
- Truke, a tool to rescue corrupted gene symbols (Miguel A. Peinado's lab, 2017). Source, paper.
- Chainy, a Web tool to process real-time PCR data (Miguel A. Peinado's lab, 2017). Source, paper, supplementary material.
- Alu ontology, a knowledgebase of human Alu elements (Miguel A. Peinado's lab, 2016). Source, paper.
- Wanderer, DNA methylation and expression browser for TCGA data (Miguel A. Peinado's lab, 2015). Source, paper, manual.
- Methylation plotter, Web tool to visualize DNA methylation data (Miguel A. Peinado's lab, 2014). Source, paper, manual.
- pcrEfficiency, a tool to design PCR primers while predicting their efficiency (Marcos Egea's lab, 2011). Source, paper.
- OpuntiaDB, the prickle pear EST database using pESTle (Marcos Egea's lab, 2011). Source, paper, documentation.
Ongoing
- repeats, a scRNA-seq workflow to quantify repetitive elements (Mark D. Robinson lab, 2021). Source.
- cg_shadows, a caller for DNA methylation agreement from WGBS (Tuncay Baubec lab, 2018).
- Zest, a pancancer expression/DNA methylation bulk correlator (Miguel A. Peinado's lab, 2017).
- Maple, a tool to map dominant mutants using RNASeq data (2016).
- Unnamed, repetitive elements expression quantification by RNASeq (Miguel A. Peinado's lab, 2016).
- HeRMes, a platform for QPCR high resolution melting data analysis (2012).
Analysis
- hyppocampus_stems, scRNA-seq stem cells, adult mouse hyppocampus (Sebastian Jessberger's lab, 2021). Source, paper.
- cg_context, do DNMTs show sequence preference? (Tuncay Baubec's lab, 2020). Source, paper.
- Bioinfo snippets, simple WGBS/expression analysis (Tuncay Baubec's lab, 2019). Source.
- Co-methylations, on colon cancer co-methylation (Miguel A. Peinado's lab, 2018). Source.
- KLKs, Buj et al. (Mireia Jordà 's and Miguel A. Peinado's labs, 2017). Source, paper.
- QAlu, a cancer biomarker design workflow (Miguel A. Peinado's lab, 2016). Source, paper.
- Circ, circular RNAs pipeline (Miguel A. Peinado's lab, 2016). Source.
- pESTle, Storage, applications, interfaces and Web frontend for expressed sequence tags (ESTs) data (Marcos Egea's lab, 2011). PhD thesis excerpt.
Snippets
- Compara_tfbs, TFBS discovery (FIMO) on comparative genomics (Compara) data (Miguel A. Peinado's lab, 2013). Source.