Maria Katsantoni

RNA-Seq analysis made easy

Maria Katsantoni, Foivos Gypas, Christina Herrmann, Dominik Bürri et autres

You have some RNA-Seq samples and want to know what's in them? You urgently need to get these RNA-Seq results but your resident bioinformatician is on vacation — again? You have an extensive SRA query with hundreds of libraries to analyze and …

ch (code pays fourni par la source)

Peer Review Report For: ZARP: A user-friendly and versatile RNA-seq analysis workflow [version 1; peer review: 2 approved with reservations]

Maria Katsantoni, Foivos Gypas, Christina Herrmann, Dominik Bürri et autres

Background RNA sequencing (RNA-seq) is a widely used technique in many scientific studies. Given the plethora of models and software packages that have been developed for processing and analyzing RNA-seq datasets, choosing the most appropriate ones is a time-consuming process that requires …

ch (code pays fourni par la source)

ZARP: A user-friendly and versatile RNA-seq analysis workflow

Maria Katsantoni, Foivos Gypas, Christina Herrmann, Dominik Bürri et autres

Background RNA sequencing (RNA-seq) is a widely used technique in many scientific studies. Given the plethora of models and software packages that have been developed for processing and analyzing RNA-seq datasets, choosing the most appropriate ones is a time-consuming process that requires …

ch (code pays fourni par la source)

Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data

Sam Bryce-Smith, Dominik Bürri, Matthew R. Gazzara, Christina Herrmann et autres

The tremendous rate with which data is generated and analysis methods emerge makes it increasingly difficult to keep track of their domain of applicability, assumptions, limitations, and consequently, of the efficacy and precision with which they solve specific tasks. Therefore, there is …

gb, ch, us, sg, es, de, nl (code pays fourni par la source)

Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data

Sam Bryce-Smith, Dominik Bürri, Matthew R. Gazzara, Christina Herrmann et autres

The tremendous rate with which data is generated and analysis methods emerge makes it increasingly difficult to keep track of their domain of applicability, assumptions, and limitations and consequently, of the efficacy and precision with which they solve specific tasks. Therefore, there …

gb, ch, us, sg, es, de, nl (code pays fourni par la source)

APAeval: Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data

Sam Bryce-Smith, Dominik Bürri, Matthew R. Gazzara, Christina Herrmann et autres

This repository contains data used for APAeval, a community effort to benchmark algorithms that identify and quantify alternative polyadenylation from RNA-seq data. The abstract follows: Abstract: The tremendous rate with which data is generated and analysis methods emerge makes it increasingly difficult …

ZARP - RNA-Seq analysis made easy!

Maria Katsantoni, Fovios Gypas, Christina Herrmann, Dominik Bürri et autres

You have some RNA-Seq samples and want to know what's in them? You urgently need those results but your resident bioinformatician is on vacation — again? You have an extensive SRA query with hundreds of libraries to analyze and you don't know …

ch (code pays fourni par la source)

Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs

Maria Katsantoni, Erik van Nimwegen, Mihaela Zavolan

We present RCRUNCH, an end-to-end solution to CLIP data analysis for identification of binding sites and sequence specificity of RNA-binding proteins. RCRUNCH can analyze not only reads that map uniquely to the genome but also those that map to multiple genome locations …

ch (code pays fourni par la source)

Additional file 6 of Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs

Maria Katsantoni, Erik van Nimwegen, Mihaela Zavolan

Additional file 6.

ch (code pays fourni par la source)

Additional file 3 of Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs

Maria Katsantoni, Erik van Nimwegen, Mihaela Zavolan

Additional file 3.

ch (code pays fourni par la source)

Additional file 2 of Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs

Maria Katsantoni, Erik van Nimwegen, Mihaela Zavolan

Additional file 2.

ch (code pays fourni par la source)

Additional file 5 of Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs

Maria Katsantoni, Erik van Nimwegen, Mihaela Zavolan

Additional file 5.

ch (code pays fourni par la source)