Izaskun Mallona
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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.

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