CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis

ArrayPipe: a flexible processing pipeline for microarray data

A number of microarray analysis software packages exist already; however, none combines the user-friendly features of a web-based interface with potential ability to analyse multiple arrays at once using flexible analysis steps. The ArrayPipe web server (freely available at www.pathogenomics.ca/arraypipe) allows the automated application of complex analyses to microarray data which can range fr...

A Flexible Pipeline for Experimental Design, Processing, and Analysis of Microarray Data

We created a web-based microarray data analysis pipeline for managing the volumes of data created by production microarray experiments. Experiments are formalized by grouping array data into hierarchies based on types such as 'dye swap' or 'replicate.' Grouping determines the analysis to be performed and enables the tool to automatically generate reports and charts appropriate to the experiment...

A Flexible NLP Pipeline for Computational Narratology

Temporal dependencies reveal interesting insights into the semantic discourse structure of narrative texts. The investigations of literary scientists are, as of today, mostly based on labor-intensive manual annotations. Computational Narratology, an important subtopic of the Digital Humanities, aims at facilitating annotations and supporting literary scientists with their analyses. According to...

Flexible Data Analysis Pipeline for High-Confidence Proteogenomics

Proteogenomics leverages information derived from proteomic data to improve genome annotations. Of particular interest are "novel" peptides that provide direct evidence of protein expression for genomic regions not previously annotated as protein-coding. We present a modular, automated data analysis pipeline aimed at detecting such "novel" peptides in proteomic data sets. This pipeline implemen...

Synthesis and Analysis: A Flexible Technique for Processing Command Language