├── .Rhistory ├── .gitattributes ├── LICENSE ├── Readme.md ├── Rplot001.jpg ├── data ├── RNAseq │ ├── 19F │ │ ├── wtKanClean │ │ │ ├── 19F-NDC120min-19F-KAN120min-DGE-results.csv │ │ │ ├── 19F-NDC20min-19F-KAN20min-DGE-results.csv │ │ │ ├── 19F-NDC45min-19F-KAN45min-DGE-results.csv │ │ │ ├── W19F-KAN10min-W19F-NDC10min-DGE-results.csv │ │ │ ├── W19F-KAN120min-W19F-NDC120min-DGE-results.csv │ │ │ ├── W19F-KAN150min-W19F-NDC150min-DGE-results.csv │ │ │ ├── W19F-KAN180min-W19F-NDC180min-DGE-results.csv │ │ │ ├── W19F-KAN20min-W19F-NDC20min-DGE-results.csv │ │ │ ├── W19F-KAN210min-W19F-NDC210min-DGE-results.csv │ │ │ ├── W19F-KAN240min-W19F-NDC240min-DGE-results.csv │ │ │ ├── W19F-KAN30min-W19F-NDC30min-DGE-results.csv │ │ │ ├── W19F-KAN45min-W19F-ND45min-DGE-results.csv │ │ │ ├── W19F-KAN60min-W19F-NDC60min-DGE-results.csv │ │ │ └── W19F-KAN90min-W19F-NDC90min-DGE-results.csv │ │ ├── wtLevo │ │ │ ├── 19F-11L120MIN-19F-NDC120MIN-DGE-results.csv │ │ │ ├── 19F-11L150MIN-19F-NDC150MIN-DGE-results.csv │ │ │ ├── 19F-11L180MIN-19F-NDC180MIN-DGE-results.csv │ │ │ ├── 19F-11L210MIN-19F-NDC210MIN-DGE-results.csv │ │ │ ├── 19F-11L240MIN-19F-NDC240MIN-DGE-results.csv │ │ │ ├── 19F-11L30MIN-19F-NDC30MIN-DGE-results.csv │ │ │ ├── 19F-11L60MIN-19F-NDC60MIN-DGE-results.csv │ │ │ └── 19F-11L90MIN-19F-NDC90MIN-DGE-results.csv │ │ ├── wtPen │ │ │ ├── 19F-10MINPEN3-19F-10MINNDC-DGE-results.csv │ │ │ ├── 19F-120MINPEN3-19F-120MINNDC-DGE-results.csv │ │ │ ├── 19F-20MINPEN3-19F-20MINNDC-DGE-results.csv │ │ │ ├── 19F-30MINPEN3-19F-30MINNDC-DGE-results.csv │ │ │ ├── 19F-45MINPEN3-19F-45MINNDC-DGE-results.csv │ │ │ ├── 19F-60MINPEN3-19F-60MINNDC-DGE-results.csv │ │ │ └── 19F-90MINPEN3-19F-90MINNDC-DGE-results.csv │ │ ├── wtRif │ │ │ ├── 19F-NDC10MIN-19F-RIF10MIN-DGE-results.csv │ │ │ ├── 19F-NDC120MIN-19F-RIF120MIN-DGE-results.csv │ │ │ ├── 19F-NDC20MIN-19F-RIF20MIN-DGE-results.csv │ │ │ ├── 19F-NDC30MIN-19F-RIF30MIN-DGE-results.csv │ │ │ ├── 19F-NDC45MIN-19F-RIF45MIN-DGE-results.csv │ │ │ ├── 19F-NDC60MIN-19F-RIF60MIN-DGE-results.csv │ │ │ └── 19F-NDC90MIN-19F-RIF90MIN-DGE-results.csv │ │ └── wtVanc │ │ │ ├── 19F-NDC10MIN-19F-VNC10MIN-DGE-results.csv │ │ │ ├── 19F-NDC120MIN-19F-VNC120MIN-DGE-results.csv │ │ │ ├── 19F-NDC20MIN-19F-VNC20MIN-DGE-results.csv │ │ │ ├── 19F-NDC30MIN-19F-VNC30MIN-DGE-results.csv │ │ │ ├── 19F-NDC45MIN-19F-VNC45MIN-DGE-results.csv │ │ │ ├── 19F-NDC60MIN-19F-VNC60MIN-DGE-results.csv │ │ │ └── 19F-NDC90MIN-19F-VNC90MIN-DGE-results.csv │ └── TIGR4 │ │ ├── wtKan │ │ ├── T4-NDC30min-T4-KAN30min-DGE-results.csv │ │ ├── T4-NDC45min-T4-KAN45min-DGE-results.csv │ │ ├── T4-NDC60min-T4-KAN60min-DGE-results.csv │ │ ├── WT4-KAN10min-WT4-NDC10min-DGE-results.csv │ │ ├── WT4-KAN120min-WT4-NDC120min-DGE-results.csv │ │ ├── WT4-KAN150min-WT4-NDC150min-DGE-results.csv │ │ ├── WT4-KAN180min-WT4-NDC180min-DGE-results.csv │ │ ├── WT4-KAN20min-WT4-NDC20min-DGE-results.csv │ │ ├── WT4-KAN210min-WT4-NDC210min-DGE-results.csv │ │ ├── WT4-KAN240min-WT4-NDC240min-DGE-results.csv │ │ ├── WT4-KAN30min-WT4-NDC30min-DGE-results.csv │ │ ├── WT4-KAN45min-WT4-NDC45min-DGE-results.csv │ │ ├── WT4-KAN60min-WT4-NDC60min-DGE-results.csv │ │ └── WT4-KAN90min-WT4-NDC90min-DGE-results.csv │ │ ├── wtLevo │ │ ├── WT4LVX10MINmerge.csv │ │ ├── WT4LVX120MINmerge.csv │ │ ├── WT4LVX180MINmerge.csv │ │ ├── WT4LVX20MINmerge.csv │ │ ├── WT4LVX30MINmerge.csv │ │ ├── WT4LVX45MINmerge.csv │ │ ├── WT4LVX60MINmerge.csv │ │ └── WT4LVX90MINmerge.csv │ │ ├── wtPen │ │ ├── T4-NDC10MIN-T4-PEN10MIN-DGE-results.csv │ │ ├── T4-NDC120MIN-T4-PEN120MIN-DGE-results.csv │ │ ├── T4-NDC20MIN-T4-PEN20MIN-DGE-results.csv │ │ ├── T4-NDC30MIN-T4-PEN30MIN-DGE-results.csv │ │ ├── T4-NDC45MIN-T4-PEN45MIN-DGE-results.csv │ │ ├── T4-NDC60MIN-T4-PEN60MIN-DGE-results.csv │ │ └── T4-NDC90MIN-T4-PEN90MIN-DGE-results.csv │ │ ├── wtRif │ │ ├── T4-NDC10MIN-T4-RIF10MIN-DGE-results.csv │ │ ├── T4-NDC120MIN-T4-RIF120MIN-DGE-results.csv │ │ ├── T4-NDC20MIN-T4-RIF20MIN-DGE-results.csv │ │ ├── T4-NDC30MIN-T4-RIF30MIN-DGE-results.csv │ │ ├── T4-NDC45MIN-T4-RIF45MIN-DGE-results.csv │ │ ├── T4-NDC60MIN-T4-RIF60MIN-DGE-results.csv │ │ └── T4-NDC90MIN-T4-RIF90MIN-DGE-results.csv │ │ └── wtVanco24 │ │ ├── wT4-NV10min-wT4-024V10min-DGE-results.csv │ │ ├── wT4-NV20min-wT4-024V20min-DGE-results.csv │ │ ├── wT4-NV30min-wT4-024V30min-DGE-results.csv │ │ ├── wT4-NV45min-wT4-024V45min-DGE-results.csv │ │ ├── wT4-NV60min-wT4-024V60min-DGE-results.csv │ │ └── wT4-NV90min-wT4-024V90min-DGE-results.csv ├── Tn-seq │ ├── 19F-E18NoAB-19F-E18Rif006.csv │ ├── 19F_KAN-TVO_v2.csv │ ├── 19F_LVX-TVO_v2.csv │ ├── 19F_Pen-TVO_v2.csv │ ├── 19F_VNC-TVO_v2.csv │ ├── 2394_KAN_TVO_v2.csv │ ├── 2394_LEVO_TVO_v2.csv │ ├── 2394_PEN_TVO_v2.csv │ ├── 2394_VANC_TVO_v2.csv │ └── T4-E13-NoAb-T4-E13-Rif07.csv ├── exptsheet.csv ├── metadata │ ├── 19F_metadata.csv │ ├── Mtb_metadata.csv │ └── T4_metadata.csv ├── microarray │ ├── Mtb_hypoxia_Day1vs0.csv │ ├── Mtb_hypoxia_Day2vs0.csv │ ├── Mtb_hypoxia_Day3vs0.csv │ ├── Mtb_hypoxia_Day5vs0.csv │ └── Mtb_hypoxia_Day7vs0.csv ├── network │ ├── Metab19F_Edges.csv │ ├── MetabT4_Edges.csv │ ├── Mtb_regulatory_Edges.csv │ └── T4_Regulatory_Edges.csv └── proteomics │ ├── Mtb_D05.csv │ ├── Mtb_D10.csv │ └── Mtb_D20.csv ├── scripts ├── files_validator.R ├── get_ci.R ├── make_RNAseq_longtable.R └── make_node_table.R ├── server.R └── ui.R /.Rhistory: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dsurujon/ShinyOmics/HEAD/.Rhistory -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/dsurujon/ShinyOmics/HEAD/.gitattributes -------------------------------------------------------------------------------- /LICENSE: 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