PanDrugs

PanDrugs provides a platform to guide the selection of therapies from the results of genome-wide studies in cancer disease.

Using 4 alternative inputs (e.g. standard VCF files, RNK files, gene list and drug query), PanDrugs identify actionable molecular alterations and prioritize drugs by calculating gene-drug scores which takes into account: i) genomic feature evidence by mutation impact score; ii) target pathway context; iii) drug approval status (FDA, clinical trial or experimental small molecule inhibitors) and iv) manually-curated pharmacological information retrieved from the literature.

PanDrugs scores combines biological and clinical relevance of the genes and their susceptibility to be targeted reflecting the strength or evidence level of the gene-drug association in order to assist the clinical decision making.

 
DEWE

DEWE (Differential Expression Workflow Executor) is an open-source software to perform genetic differential expression analysis of RNA-Seq data.

DEWE offers built-in, easy-to-configure workflows that facilitate the execution of DE analyses. Currently, DEWE provides two differential expression analysis workflows: HISAT2, StringTie and Ballgown and Bowtie2, StringTie and R libraries (Ballgown and edgeR).

A key feature of DEWE is the interactive results management and visualisation. The main results of the execution of a built-in workflow are the outputs provided by Ballgown or edgeR. These outputs are automatically visualised in DEWE after the workflow execution and they can be reopened at any later time.

 
SEDA

SEDA (SEquence DAtaset builder) is an open source application for processing FASTA files containing DNA and protein sequences.

Among other functions, SEDA allows you to:

  • Filter sequences based on different criteria (including text patterns).
  • Translate nucleic acid sequences into amino acid sequences.
  • Execute Blast analyses.
  • Remove duplicated sequences.
  • Sort, merge, split or reformat files.
 
Gleukos

Gleukos is a new public Web-based resource that aims to provide a comprehensive portrait of the glycolytic abilities of bacteria, in articular those encrypted in the protein complement of the human microbiome.

This project addresses the understanding of human gastrointestinal microbiota and its role in human physiology. Large amount of data point to the involvement of intestinal bacteria in the initiation and amplification of inflammatory diseases, an in the maintenance of a healthy state. This has been driven by new evidence of the crucial role played by these communities in host health, and by accelerated progress based on new -omics methodologies. Many scientific publications support dysbiosis as one of the causes (or consequences) of gastrointestinal disorders. Our hypothesis is that a bioinformatics approach is suitable for generating the proper experimental conditions that allow the cultivation of specific groups of strict gut anaerobes that are underrepresented in gastrointestinal disorders.

 
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