handle of '#' character in input file by proteore tools

[davidchristiany]

kegg maps a été mis à jour pour prendre en compte les lignes contenant un '#', dans un soucis d'harmonisation, il faut que tous les outils ne considèrent plus le '#' comme le début d'un commentaire et qu'ils les supprime du fichier output.

[davidchristiany]

liste des outils prenant en charge les '#' dans le header

ProteoRE

• [x] id converter
• [x] Filter by keywords and/or numerical value
• [x] Venn diagram [JVenn]
• [x] HeatMap (Cluster and visualize the results)

Human Annotation

• [x] Get expression profiles by (normal or tumor) tissue/cell type [Human Protein Atlas]
• [x] Add expression data (RNAseq or Immuno-assays)[Human Protein Atlas]
• [x] Add protein features [neXtProt]
• [x] Get MS/MS observations in tissue/fluid [Peptide Atlas]
• [x] Build tissue-specific expression dataset [Human Protein Atlas] (no input required)

Mouse Annotation

• [x] Add protein features (Mouse) [UniProt]

Go terms Analysis

• [x] Statistical analysis of functional profiles (Human, Mouse) [goProfiles]
• [x] Enrichment analysis for Gene Ontology (Human, Mouse, Rat)[topGO]
• [x] GO terms classification and enrichment analysis (Human, Mouse, Rat)[clusterProfiler]
• [x] GO terms profiles comparison

Pathway Analysis

• [x] Query pathway database [Reactome]
• [x] Pathways identification and coverage [KEGG]
• [x] Pathways visualization of (differentially expressed) genes/proteins [KEGG]
• [x] Build Protein-Protein interaction network [BioGRID, BioPlex, HuMAP]