Assays

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1 Assay visible to you, out of a total of 1

_A_02_Nb_datasets-CoExp

SUSPHIRE - Sustainable Bioproduction of Pheromones for Insect Pest Control in Agriculture

Short Name: 02_Nb_datasets-CoExp Assay Class: DRY Assay Type: CoExp Title: CoExp analysis using available Nb RNA-seq datasets Description: CoExpNetViz analysis using SUSPHIRE SxPv1.0 expression data together with available RNA-Seq datsets from Nicotiana benthamiana - average logCPM values or clculated logFCs were used as inputs to generate coexpression networks based on given baits. pISA Assay creation date: 2020-07-03 pISA Assay creator: Mojca JuterĹˇek Phenodata: None Featuredata: Data:

Submitter: Marko Petek

Assay type: Experimental Assay Type

Technology type: Technology Type

Investigation: _I_T21_SXPsysbio

Study: _S_P4_CoExpNetViz

Organisms: No organisms

SOPs: No SOPs

Data files: _ASSAY_METADATA.TXT, input/01_Nb_datasets/Nb_datasets.xlsx, input/01_Nb_datasets/Nb_runs.txt, input/01_Nb_datasets/Nb_runs.xlsx, input/03_STAR_mapping/R_featureCounts_script.txt, input/03_STAR_mapping/STAR_commands.txt, input/03_STAR_mapping/deinterleave_command.txt, input/04_featureCounts/Counts.txt, input/04_featureCounts/Counts.xlsx, input/04_featureCounts/SexyPlant_counts_STAR_PE..., input/04_featureCounts/SexyPlant_counts_STAR_SE..., input/05_R_normalization/ReplicatesGrouping.xlsx, input/05_R_normalization/aver.lcpm_woBadies.txt, input/05_R_normalization/aver_lcpm_wGenes.txt, input/06_Baits/Anthocyanin_baits.txt, input/06_Baits/Gibberelin_baits.txt, input/06_Baits/Jasmonate_baits.txt, input/06_Baits/Lipid_baits.txt, input/07_InputByDE/AllLogFC/NbDataset_logFC-cal..., input/07_InputByDE/AllLogFC/NbDataset_logFC.txt, input/07_InputByDE/AllLogFC/PRJNA186900_logFC-c..., input/07_InputByDE/AllLogFC/PRJNA186900_logFC.txt, input/07_InputByDE/AllLogFC/PRJNA188486_logFC-c..., input/07_InputByDE/AllLogFC/PRJNA188486_logFC.txt, input/07_InputByDE/AllLogFC/PRJNA258306_logFC-c..., input/07_InputByDE/AllLogFC/PRJNA258306_logFC.txt, input/07_InputByDE/AllLogFC/PRJNA304339_logFC-c..., input/07_InputByDE/AllLogFC/PRJNA304339_logFC.txt, input/07_InputByDE/AllLogFC/PRJNA326507_logFC-f..., input/07_InputByDE/AllLogFC/PRJNA326507_logFC.txt, input/07_InputByDE/AllLogFC/PRJNA385234_logFC-c..., input/07_InputByDE/AllLogFC/PRJNA385234_logFC.txt, input/07_InputByDE/AllLogFC/PRJNA389675_PE_logF..., input/07_InputByDE/AllLogFC/PRJNA389675_PE_logF..., input/07_InputByDE/AllLogFC/PRJNA389675_SE_logF..., input/07_InputByDE/AllLogFC/PRJNA389675_SE_logF..., input/07_InputByDE/AllLogFC/PRJNA412101_logFC-c..., input/07_InputByDE/AllLogFC/PRJNA412101_logFC.txt, input/07_InputByDE/AllLogFC/PRJNA429737_logFC-f..., input/07_InputByDE/AllLogFC/PRJNA429737_logFC.txt, input/07_InputByDE/AllLogFC/PRJNA481441_logFC-f..., input/07_InputByDE/AllLogFC/PRJNA481441_logFC.txt, input/07_InputByDE/AllLogFC/PRJNA491789_logFC-f..., input/07_InputByDE/AllLogFC/PRJNA491789_logFC.txt, input/07_InputByDE/AllLogFC/PRJNA507084_logFC-f..., input/07_InputByDE/AllLogFC/PRJNA507084_logFC.txt, input/07_InputByDE/AllLogFC/PRJNA564947_logFC-f..., input/07_InputByDE/AllLogFC/PRJNA564947_logFC.txt, input/07_InputByDE/AllLogFC/SUSPHIREdata_logFC-..., input/07_InputByDE/AllLogFC/all_wo491783_logFC.txt, input/07_InputByDE/AllLogFC/clean_logFC.txt, input/07_InputByDE/ExpNoReplicates/NbDataset/Nb..., input/07_InputByDE/ExpNoReplicates/NbDataset/Nb..., input/07_InputByDE/ExpNoReplicates/NbDataset/Nb..., input/07_InputByDE/ExpNoReplicates/NbDataset/Nb..., input/07_InputByDE/ExpNoReplicates/PRJNA186900/..., input/07_InputByDE/ExpNoReplicates/PRJNA186900/..., input/07_InputByDE/ExpNoReplicates/PRJNA186900/..., input/07_InputByDE/ExpNoReplicates/PRJNA186900/..., input/07_InputByDE/ExpNoReplicates/PRJNA188486/..., input/07_InputByDE/ExpNoReplicates/PRJNA188486/..., input/07_InputByDE/ExpNoReplicates/PRJNA188486/..., input/07_InputByDE/ExpNoReplicates/PRJNA188486/..., input/07_InputByDE/ExpNoReplicates/PRJNA258306/..., input/07_InputByDE/ExpNoReplicates/PRJNA258306/..., input/07_InputByDE/ExpNoReplicates/PRJNA258306/..., input/07_InputByDE/ExpNoReplicates/PRJNA258306/..., input/07_InputByDE/ExpNoReplicates/PRJNA304339/..., input/07_InputByDE/ExpNoReplicates/PRJNA304339/..., input/07_InputByDE/ExpNoReplicates/PRJNA304339/..., input/07_InputByDE/ExpNoReplicates/PRJNA304339/..., input/07_InputByDE/ExpNoReplicates/PRJNA385234/..., input/07_InputByDE/ExpNoReplicates/PRJNA385234/..., input/07_InputByDE/ExpNoReplicates/PRJNA385234/..., input/07_InputByDE/ExpNoReplicates/PRJNA385234/..., input/07_InputByDE/ExpNoReplicates/PRJNA412101/..., input/07_InputByDE/ExpNoReplicates/PRJNA412101/..., input/07_InputByDE/ExpNoReplicates/PRJNA412101/..., input/07_InputByDE/ExpNoReplicates/PRJNA412101/..., input/07_InputByDE/ExpNoReplicates/README.txt, input/07_InputByDE/ExpWithReplicates/PRJNA32650..., input/07_InputByDE/ExpWithReplicates/PRJNA32650..., input/07_InputByDE/ExpWithReplicates/PRJNA32650..., input/07_InputByDE/ExpWithReplicates/PRJNA32650..., input/07_InputByDE/ExpWithReplicates/PRJNA38967..., input/07_InputByDE/ExpWithReplicates/PRJNA38967..., input/07_InputByDE/ExpWithReplicates/PRJNA38967..., input/07_InputByDE/ExpWithReplicates/PRJNA38967..., input/07_InputByDE/ExpWithReplicates/PRJNA38967..., input/07_InputByDE/ExpWithReplicates/PRJNA38967..., input/07_InputByDE/ExpWithReplicates/PRJNA38967..., input/07_InputByDE/ExpWithReplicates/PRJNA42973..., input/07_InputByDE/ExpWithReplicates/PRJNA42973..., input/07_InputByDE/ExpWithReplicates/PRJNA42973..., input/07_InputByDE/ExpWithReplicates/PRJNA48144..., input/07_InputByDE/ExpWithReplicates/PRJNA48144..., input/07_InputByDE/ExpWithReplicates/PRJNA48144..., input/07_InputByDE/ExpWithReplicates/PRJNA49178..., input/07_InputByDE/ExpWithReplicates/PRJNA49178..., input/07_InputByDE/ExpWithReplicates/PRJNA49178..., input/07_InputByDE/ExpWithReplicates/PRJNA50708..., input/07_InputByDE/ExpWithReplicates/PRJNA50708..., input/07_InputByDE/ExpWithReplicates/PRJNA50708..., input/07_InputByDE/ExpWithReplicates/PRJNA56494..., input/07_InputByDE/ExpWithReplicates/PRJNA56494..., input/07_InputByDE/ExpWithReplicates/PRJNA56494..., input/07_InputByDE/ExpWithReplicates/README.txt, input/07_InputByDE/ExpWithReplicates/SUSPHIREda..., input/07_InputByDE/ExpWithReplicates/SUSPHIREda..., input/07_InputByDE/ExpWithReplicates/SUSPHIREda..., output/2020-11-20/Gibberelin_baits/Edges_export..., output/2020-11-20/Gibberelin_baits/Gibberelins_..., output/2020-11-20/Gibberelin_baits/Network/READ..., output/2020-11-20/Gibberelin_baits/Network/aver..., output/2020-11-20/Gibberelin_baits/Network/aver..., output/2020-11-20/Gibberelin_baits/Network/aver..., output/2020-11-20/Gibberelin_baits/Network/corr..., output/2020-11-20/Gibberelin_baits/Nodes_export..., output/2020-11-20/Jasmonate_baits/Edges_export.csv, output/2020-11-20/Jasmonate_baits/Jasmonates_cu..., output/2020-11-20/Jasmonate_baits/Network/READM..., output/2020-11-20/Jasmonate_baits/Network/aver...., output/2020-11-20/Jasmonate_baits/Network/aver...., output/2020-11-20/Jasmonate_baits/Network/aver...., output/2020-11-20/Jasmonate_baits/Network/corre..., output/2020-11-20/Jasmonate_baits/Nodes_export.csv, output/2020-11-20/Lipid_baits/Edges_export.csv, output/2020-11-20/Lipid_baits/LipidBaits_curate..., output/2020-11-20/Lipid_baits/Network/README.txt, output/2020-11-20/Lipid_baits/Network/aver.lcpm..., output/2020-11-20/Lipid_baits/Network/aver.lcpm..., output/2020-11-20/Lipid_baits/Network/aver.lcpm..., output/2020-11-20/Lipid_baits/Network/correlati..., output/2020-11-20/Lipid_baits/Nodes_export.csv, output/2021-06-02/Jasmonates_curated1.xlsx, output/2021-06-02/README.txt, output/2021-06-02/clean_logFC.txt.corr_sample_c..., output/2021-06-02/clean_logFC.txt.corr_sample_h..., output/2021-06-02/clean_logFC.txt.sim_mat.txt, output/2021-06-02/correlations_per_family.txt, output/2021-06-02/nodeTable.csv, output/2021-06-02/nodeTable.xlsx, output/2021-06-21/Jasmonate_baits/Curated_JA.xlsx, output/2021-06-21/Jasmonate_baits/edgesExport.csv, output/2021-06-21/Jasmonate_baits/network/READM..., output/2021-06-21/Jasmonate_baits/network/clean..., output/2021-06-21/Jasmonate_baits/network/clean..., output/2021-06-21/Jasmonate_baits/network/clean..., output/2021-06-21/Jasmonate_baits/network/corre..., output/2021-06-21/Jasmonate_baits/nodesExport.csv, output/2022-01-26/anthocyanin.xlsx, output/2022-01-26/network_anthocyanin/network/R..., output/2022-01-26/network_anthocyanin/network/c..., output/2022-01-26/network_anthocyanin/network/c..., output/2022-01-26/network_anthocyanin/network/c..., output/2022-01-26/network_anthocyanin/network/c..., output/2022-01-26/network_anthocyanin/node_tabl..., output/2022-01-26/network_anthocyanin_cpm/netwo..., output/2022-01-26/network_anthocyanin_cpm/netwo..., output/2022-01-26/network_anthocyanin_cpm/netwo..., output/2022-01-26/network_anthocyanin_cpm/netwo..., output/2022-01-26/network_anthocyanin_cpm/netwo..., output/2022-01-26/network_anthocyanin_cpm/node_..., scripts/R_featureCounts_script.txt, scripts/STAR_commands.txt, scripts/deinterleave_command.txt

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Created: 9th Apr 2022 at 18:47, Last updated: 21st Sep 2022 at 10:45

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