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    SourceForge net documentation for the confero command line interface (cli)
    Biological knowledge building process enabled by <t>Confero</t> which enhances the standard omics analysis workflow. The left loop depicts the typical omics workflow from data generation, processing, and statistical analysis followed by downstream computational analysis and biological interpretation leading to new hypothesis generation. With Confero in place a second loop is added where statistical analysis results are automatically processed and new a priori biological knowledge in the form of gene set is stored. This database of knowledge grows with new experimental and external data and is leveraged by integrated tools for biological interpretation of current and future studies. The overall process drives and enhances the experimental research lifecycle.
    Documentation For The Confero Command Line Interface (Cli), supplied by SourceForge net, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/documentation for the confero command line interface (cli)/product/SourceForge net
    Average 90 stars, based on 1 article reviews
    documentation for the confero command line interface (cli) - by Bioz Stars, 2026-03
    90/100 stars

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    1) Product Images from "Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data"

    Article Title: Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-14-514

    Biological knowledge building process enabled by Confero which enhances the standard omics analysis workflow. The left loop depicts the typical omics workflow from data generation, processing, and statistical analysis followed by downstream computational analysis and biological interpretation leading to new hypothesis generation. With Confero in place a second loop is added where statistical analysis results are automatically processed and new a priori biological knowledge in the form of gene set is stored. This database of knowledge grows with new experimental and external data and is leveraged by integrated tools for biological interpretation of current and future studies. The overall process drives and enhances the experimental research lifecycle.
    Figure Legend Snippet: Biological knowledge building process enabled by Confero which enhances the standard omics analysis workflow. The left loop depicts the typical omics workflow from data generation, processing, and statistical analysis followed by downstream computational analysis and biological interpretation leading to new hypothesis generation. With Confero in place a second loop is added where statistical analysis results are automatically processed and new a priori biological knowledge in the form of gene set is stored. This database of knowledge grows with new experimental and external data and is leveraged by integrated tools for biological interpretation of current and future studies. The overall process drives and enhances the experimental research lifecycle.

    Techniques Used:

    Confero platform overview. Depicts where Confero fits into a typical high-throughput transcriptomics analysis workflow. Contrast data is fed into the platform after the statistical analysis step where it is then converted to idMAPS format and loaded using Confero tools. Contrast data is automatically processed and stored and gene sets are extracted. Data can be analyzed for gene set enrichment and results can be used in other Confero tools or exported for other analyses.
    Figure Legend Snippet: Confero platform overview. Depicts where Confero fits into a typical high-throughput transcriptomics analysis workflow. Contrast data is fed into the platform after the statistical analysis step where it is then converted to idMAPS format and loaded using Confero tools. Contrast data is automatically processed and stored and gene sets are extracted. Data can be analyzed for gene set enrichment and results can be used in other Confero tools or exported for other analyses.

    Techniques Used: High Throughput Screening Assay

    Screenshot of Confero platform integrated in Galaxy. Confero platform is a standalone application that can be used via the command line. However, for non-programmatic users and to provide flexibility, Confero platform has been integrated into Galaxy. The window shows three main frames: 1) the first frame on the left contains all Confero tools (also see Additional file : Table S1) to import data (DATA IMPORT), manage and export data from Confero (DATA MANAGEMENT AND EXPORT), run GSEA or ORA and manage results (FUNCTIONAL ENRICHMENT ANALYSIS MODULE); 2) the second frame in the middle generally displays the web page with the menu when selecting a tool, and results once the job is done; 3) the third frame on the right contains all the history of actions/results performed during an analysis. This history is saved and the user can investigate the results of the analysis at any time. The user has also the possibility to share the history with other users that have an account in Galaxy.
    Figure Legend Snippet: Screenshot of Confero platform integrated in Galaxy. Confero platform is a standalone application that can be used via the command line. However, for non-programmatic users and to provide flexibility, Confero platform has been integrated into Galaxy. The window shows three main frames: 1) the first frame on the left contains all Confero tools (also see Additional file : Table S1) to import data (DATA IMPORT), manage and export data from Confero (DATA MANAGEMENT AND EXPORT), run GSEA or ORA and manage results (FUNCTIONAL ENRICHMENT ANALYSIS MODULE); 2) the second frame in the middle generally displays the web page with the menu when selecting a tool, and results once the job is done; 3) the third frame on the right contains all the history of actions/results performed during an analysis. This history is saved and the user can investigate the results of the analysis at any time. The user has also the possibility to share the history with other users that have an account in Galaxy.

    Techniques Used: Functional Assay

    Screenshot of the Estrogen gene set entry in the Confero DB. Clicking on a gene set hyperlink (e.g. BMC_Bioconductor_Estrogen_PW_[Estro10]_UP) enables to access detailed information such as the rank of the genes extracted from the contrast, the Entrez gene ID, the gene symbol and description.
    Figure Legend Snippet: Screenshot of the Estrogen gene set entry in the Confero DB. Clicking on a gene set hyperlink (e.g. BMC_Bioconductor_Estrogen_PW_[Estro10]_UP) enables to access detailed information such as the rank of the genes extracted from the contrast, the Entrez gene ID, the gene symbol and description.

    Techniques Used:

    Screenshot of the report following importing and processing of the Bioconductor estrogen contrast data in Confero using Galaxy. The report shows 1) whether contrast data have been correctly imported and processed (several checks during the mapping and collapsing process reported at the top of the document (“Check/Map/Collapse Contrast Dataset Report”), 2) information on the gene sets that have been automatically extracted from each contrast and stored (UP, DN, and AR gene sets) in the Confero DB (“Gene Set Report”). As example (see also Figure ), 169, 105 and 274 most significantly up- , down- and all-regulated genes (FDR<0.05) were respectively extracted as gene sets UP, DN and AR from the contrast data “Estro10” (comparison of gene expression levels of estrogen vs control samples collected at 10h).
    Figure Legend Snippet: Screenshot of the report following importing and processing of the Bioconductor estrogen contrast data in Confero using Galaxy. The report shows 1) whether contrast data have been correctly imported and processed (several checks during the mapping and collapsing process reported at the top of the document (“Check/Map/Collapse Contrast Dataset Report”), 2) information on the gene sets that have been automatically extracted from each contrast and stored (UP, DN, and AR gene sets) in the Confero DB (“Gene Set Report”). As example (see also Figure ), 169, 105 and 274 most significantly up- , down- and all-regulated genes (FDR<0.05) were respectively extracted as gene sets UP, DN and AR from the contrast data “Estro10” (comparison of gene expression levels of estrogen vs control samples collected at 10h).

    Techniques Used: Comparison, Gene Expression, Control

    Screenshot of the Estrogen contrast dataset entry in the Confero DB. To access a database Estrogen Contrast data entry, the “View and Manage Data” tool is selected in the toolbox (left frame) and the appropriate contrast dataset name can be chosen in the available list. The entry contains information on the contrast dataset at the top (e.g. “BMC_Bioconductor_Estrogen_PW”), contrasts (e.g. “BMC_Bioconductor_Estrogen_PW_[Estro10]”) and associated gene sets at the bottom (e.g. “BMC_Bioconductor_Estrogen_PW_[Estro10]_UP”). Details and data files can be accessed via the hyperlinks. Data files can be saved locally upon needs.
    Figure Legend Snippet: Screenshot of the Estrogen contrast dataset entry in the Confero DB. To access a database Estrogen Contrast data entry, the “View and Manage Data” tool is selected in the toolbox (left frame) and the appropriate contrast dataset name can be chosen in the available list. The entry contains information on the contrast dataset at the top (e.g. “BMC_Bioconductor_Estrogen_PW”), contrasts (e.g. “BMC_Bioconductor_Estrogen_PW_[Estro10]”) and associated gene sets at the bottom (e.g. “BMC_Bioconductor_Estrogen_PW_[Estro10]_UP”). Details and data files can be accessed via the hyperlinks. Data files can be saved locally upon needs.

    Techniques Used:

    Summary of Confero Bioconductor estrogen dataset GSEA results and leveraging of leading edge genes results from Export Leading Edge Matrix tool. Grouping gene sets per biological processes and investigating the leading edge genes associated to significantly enriched gene sets enables to rapidly interpret biological events at the molecular level and raise new hypothesis that could further be experimentally verified. Red and green colors highlight normalized enrichment scores that are significantly enriched for up- or down-regulated genes, respectively.
    Figure Legend Snippet: Summary of Confero Bioconductor estrogen dataset GSEA results and leveraging of leading edge genes results from Export Leading Edge Matrix tool. Grouping gene sets per biological processes and investigating the leading edge genes associated to significantly enriched gene sets enables to rapidly interpret biological events at the molecular level and raise new hypothesis that could further be experimentally verified. Red and green colors highlight normalized enrichment scores that are significantly enriched for up- or down-regulated genes, respectively.

    Techniques Used:



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    documentation for the confero command line interface (cli)  (SourceForge net)
    90
    SourceForge net documentation for the confero command line interface (cli)
    Biological knowledge building process enabled by <t>Confero</t> which enhances the standard omics analysis workflow. The left loop depicts the typical omics workflow from data generation, processing, and statistical analysis followed by downstream computational analysis and biological interpretation leading to new hypothesis generation. With Confero in place a second loop is added where statistical analysis results are automatically processed and new a priori biological knowledge in the form of gene set is stored. This database of knowledge grows with new experimental and external data and is leveraged by integrated tools for biological interpretation of current and future studies. The overall process drives and enhances the experimental research lifecycle.
    Documentation For The Confero Command Line Interface (Cli), supplied by SourceForge net, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/documentation for the confero command line interface (cli)/product/SourceForge net
    Average 90 stars, based on 1 article reviews
    documentation for the confero command line interface (cli) - by Bioz Stars, 2026-03
    90/100 stars
    		  Buy from Supplier

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    Biological knowledge building process enabled by Confero which enhances the standard omics analysis workflow. The left loop depicts the typical omics workflow from data generation, processing, and statistical analysis followed by downstream computational analysis and biological interpretation leading to new hypothesis generation. With Confero in place a second loop is added where statistical analysis results are automatically processed and new a priori biological knowledge in the form of gene set is stored. This database of knowledge grows with new experimental and external data and is leveraged by integrated tools for biological interpretation of current and future studies. The overall process drives and enhances the experimental research lifecycle.

    Journal: BMC Genomics

    Article Title: Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data

    doi: 10.1186/1471-2164-14-514

    Figure Lengend Snippet: Biological knowledge building process enabled by Confero which enhances the standard omics analysis workflow. The left loop depicts the typical omics workflow from data generation, processing, and statistical analysis followed by downstream computational analysis and biological interpretation leading to new hypothesis generation. With Confero in place a second loop is added where statistical analysis results are automatically processed and new a priori biological knowledge in the form of gene set is stored. This database of knowledge grows with new experimental and external data and is leveraged by integrated tools for biological interpretation of current and future studies. The overall process drives and enhances the experimental research lifecycle.

    Article Snippet: The documentation for the Confero command line interface (CLI) is provided as Additional file and is also available on SourceForge ( http://sourceforge.net/projects/confero/ ).

    Techniques:

    Confero platform overview. Depicts where Confero fits into a typical high-throughput transcriptomics analysis workflow. Contrast data is fed into the platform after the statistical analysis step where it is then converted to idMAPS format and loaded using Confero tools. Contrast data is automatically processed and stored and gene sets are extracted. Data can be analyzed for gene set enrichment and results can be used in other Confero tools or exported for other analyses.

    Journal: BMC Genomics

    Article Title: Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data

    doi: 10.1186/1471-2164-14-514

    Figure Lengend Snippet: Confero platform overview. Depicts where Confero fits into a typical high-throughput transcriptomics analysis workflow. Contrast data is fed into the platform after the statistical analysis step where it is then converted to idMAPS format and loaded using Confero tools. Contrast data is automatically processed and stored and gene sets are extracted. Data can be analyzed for gene set enrichment and results can be used in other Confero tools or exported for other analyses.

    Article Snippet: The documentation for the Confero command line interface (CLI) is provided as Additional file and is also available on SourceForge ( http://sourceforge.net/projects/confero/ ).

    Techniques: High Throughput Screening Assay

    Screenshot of Confero platform integrated in Galaxy. Confero platform is a standalone application that can be used via the command line. However, for non-programmatic users and to provide flexibility, Confero platform has been integrated into Galaxy. The window shows three main frames: 1) the first frame on the left contains all Confero tools (also see Additional file : Table S1) to import data (DATA IMPORT), manage and export data from Confero (DATA MANAGEMENT AND EXPORT), run GSEA or ORA and manage results (FUNCTIONAL ENRICHMENT ANALYSIS MODULE); 2) the second frame in the middle generally displays the web page with the menu when selecting a tool, and results once the job is done; 3) the third frame on the right contains all the history of actions/results performed during an analysis. This history is saved and the user can investigate the results of the analysis at any time. The user has also the possibility to share the history with other users that have an account in Galaxy.

    Journal: BMC Genomics

    Article Title: Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data

    doi: 10.1186/1471-2164-14-514

    Figure Lengend Snippet: Screenshot of Confero platform integrated in Galaxy. Confero platform is a standalone application that can be used via the command line. However, for non-programmatic users and to provide flexibility, Confero platform has been integrated into Galaxy. The window shows three main frames: 1) the first frame on the left contains all Confero tools (also see Additional file : Table S1) to import data (DATA IMPORT), manage and export data from Confero (DATA MANAGEMENT AND EXPORT), run GSEA or ORA and manage results (FUNCTIONAL ENRICHMENT ANALYSIS MODULE); 2) the second frame in the middle generally displays the web page with the menu when selecting a tool, and results once the job is done; 3) the third frame on the right contains all the history of actions/results performed during an analysis. This history is saved and the user can investigate the results of the analysis at any time. The user has also the possibility to share the history with other users that have an account in Galaxy.

    Article Snippet: The documentation for the Confero command line interface (CLI) is provided as Additional file and is also available on SourceForge ( http://sourceforge.net/projects/confero/ ).

    Techniques: Functional Assay

    Screenshot of the Estrogen gene set entry in the Confero DB. Clicking on a gene set hyperlink (e.g. BMC_Bioconductor_Estrogen_PW_[Estro10]_UP) enables to access detailed information such as the rank of the genes extracted from the contrast, the Entrez gene ID, the gene symbol and description.

    Journal: BMC Genomics

    Article Title: Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data

    doi: 10.1186/1471-2164-14-514

    Figure Lengend Snippet: Screenshot of the Estrogen gene set entry in the Confero DB. Clicking on a gene set hyperlink (e.g. BMC_Bioconductor_Estrogen_PW_[Estro10]_UP) enables to access detailed information such as the rank of the genes extracted from the contrast, the Entrez gene ID, the gene symbol and description.

    Article Snippet: The documentation for the Confero command line interface (CLI) is provided as Additional file and is also available on SourceForge ( http://sourceforge.net/projects/confero/ ).

    Techniques:

    Screenshot of the report following importing and processing of the Bioconductor estrogen contrast data in Confero using Galaxy. The report shows 1) whether contrast data have been correctly imported and processed (several checks during the mapping and collapsing process reported at the top of the document (“Check/Map/Collapse Contrast Dataset Report”), 2) information on the gene sets that have been automatically extracted from each contrast and stored (UP, DN, and AR gene sets) in the Confero DB (“Gene Set Report”). As example (see also Figure ), 169, 105 and 274 most significantly up- , down- and all-regulated genes (FDR<0.05) were respectively extracted as gene sets UP, DN and AR from the contrast data “Estro10” (comparison of gene expression levels of estrogen vs control samples collected at 10h).

    Journal: BMC Genomics

    Article Title: Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data

    doi: 10.1186/1471-2164-14-514

    Figure Lengend Snippet: Screenshot of the report following importing and processing of the Bioconductor estrogen contrast data in Confero using Galaxy. The report shows 1) whether contrast data have been correctly imported and processed (several checks during the mapping and collapsing process reported at the top of the document (“Check/Map/Collapse Contrast Dataset Report”), 2) information on the gene sets that have been automatically extracted from each contrast and stored (UP, DN, and AR gene sets) in the Confero DB (“Gene Set Report”). As example (see also Figure ), 169, 105 and 274 most significantly up- , down- and all-regulated genes (FDR<0.05) were respectively extracted as gene sets UP, DN and AR from the contrast data “Estro10” (comparison of gene expression levels of estrogen vs control samples collected at 10h).

    Article Snippet: The documentation for the Confero command line interface (CLI) is provided as Additional file and is also available on SourceForge ( http://sourceforge.net/projects/confero/ ).

    Techniques: Comparison, Gene Expression, Control

    Screenshot of the Estrogen contrast dataset entry in the Confero DB. To access a database Estrogen Contrast data entry, the “View and Manage Data” tool is selected in the toolbox (left frame) and the appropriate contrast dataset name can be chosen in the available list. The entry contains information on the contrast dataset at the top (e.g. “BMC_Bioconductor_Estrogen_PW”), contrasts (e.g. “BMC_Bioconductor_Estrogen_PW_[Estro10]”) and associated gene sets at the bottom (e.g. “BMC_Bioconductor_Estrogen_PW_[Estro10]_UP”). Details and data files can be accessed via the hyperlinks. Data files can be saved locally upon needs.

    Journal: BMC Genomics

    Article Title: Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data

    doi: 10.1186/1471-2164-14-514

    Figure Lengend Snippet: Screenshot of the Estrogen contrast dataset entry in the Confero DB. To access a database Estrogen Contrast data entry, the “View and Manage Data” tool is selected in the toolbox (left frame) and the appropriate contrast dataset name can be chosen in the available list. The entry contains information on the contrast dataset at the top (e.g. “BMC_Bioconductor_Estrogen_PW”), contrasts (e.g. “BMC_Bioconductor_Estrogen_PW_[Estro10]”) and associated gene sets at the bottom (e.g. “BMC_Bioconductor_Estrogen_PW_[Estro10]_UP”). Details and data files can be accessed via the hyperlinks. Data files can be saved locally upon needs.

    Article Snippet: The documentation for the Confero command line interface (CLI) is provided as Additional file and is also available on SourceForge ( http://sourceforge.net/projects/confero/ ).

    Techniques:

    Summary of Confero Bioconductor estrogen dataset GSEA results and leveraging of leading edge genes results from Export Leading Edge Matrix tool. Grouping gene sets per biological processes and investigating the leading edge genes associated to significantly enriched gene sets enables to rapidly interpret biological events at the molecular level and raise new hypothesis that could further be experimentally verified. Red and green colors highlight normalized enrichment scores that are significantly enriched for up- or down-regulated genes, respectively.

    Journal: BMC Genomics

    Article Title: Confero: an integrated contrast data and gene set platform for computational analysis and biological interpretation of omics data

    doi: 10.1186/1471-2164-14-514

    Figure Lengend Snippet: Summary of Confero Bioconductor estrogen dataset GSEA results and leveraging of leading edge genes results from Export Leading Edge Matrix tool. Grouping gene sets per biological processes and investigating the leading edge genes associated to significantly enriched gene sets enables to rapidly interpret biological events at the molecular level and raise new hypothesis that could further be experimentally verified. Red and green colors highlight normalized enrichment scores that are significantly enriched for up- or down-regulated genes, respectively.

    Article Snippet: The documentation for the Confero command line interface (CLI) is provided as Additional file and is also available on SourceForge ( http://sourceforge.net/projects/confero/ ).

    Techniques: