Tools

Released

• 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

• SINCERE, a scRNA-Seq aligner to curated references (Mark D. Robinson lab, 2018).
• cg_shadows, a caller for DNA methylation agreement from WGBS (Tuncay Baubec lab, 2018).
• cg_context, sequence constraints of DNA methylation (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

• Bioinfo snippets, simple WGBS/expression analysis (Tuncay Baubec's lab, 2018). 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.

Chunks

• Compara_tfbs, TFBS discovery (FIMO) on comparative genomics (Compara) data (Miguel A. Peinado's lab, 2013). Source.