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| # NetBID 2.0 | ||
| NetBID (**Net**work-based **B**ayesian **I**nference of **D**rivers) is a data-driven system biology pipeline and toolkit for finding drivers from transcriptomics, proteomics and phosphoproteomics data, where the drivers can be either transcription factors (**TF**) or signaling factors (**SIG**). | ||
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| NetBID 2.0 is an upgraded version of [NetBID 1.0](https://github.com/jyyulab/NetBID/releases/tag/1.0.0) that has been published in [Nature]((https://www.nature.com/articles/s41586-018-0177-0)) in 2018. NetBID 2.0 inherites all the main functions from NetBID 1.0, and provides many more functions and pipelines to perform advanced end-to-end analyses. | ||
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| # Installation | ||
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| Require ```R >= 3.6.0```. Other dependencies can be found in table [https://jyyulab.github.io/NetBID/docs/pre_request](https://jyyulab.github.io/NetBID/docs/pre_request). | ||
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| Installation instructions are in [Installation section](https://jyyulab.github.io/NetBID/) of the documentation. | ||
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| # Documentation & Guided Analyses | ||
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| Instructions, documentation, and tutorials can be found at: | ||
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| + [https://jyyulab.github.io/NetBID/](https://jyyulab.github.io/NetBID/) | ||
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| A PDF manual [NetBID_manual.pdf](https://github.com/jyyulab/NetBID/blob/master/NetBID_manual.pdf) can be found in the repository. | ||
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| # Docker | ||
| We publish our lastest docker builds on DockerHub. You can pull the docker image by running the following command: | ||
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| ```$ docker pull jyyulab/netbid2:2.0.1``` | ||
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| The docker image has build-in RStudio server that can be launched by | ||
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| ```$ docker run -it netbid2:2.0.1 rserver --server-daemonize 0``` | ||
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| For interactive command line analysis, use the following command: | ||
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| ```$ docker run -it netbid2:2.0.1``` | ||
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| # Demos | ||
| Demo scripts can be found in [demo_scripts](https://github.com/jyyulab/NetBID/tree/master/demo_scripts) directory. | ||
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| ### Demo script for network generation | ||
| Summary of steps in pipeline_network_demo1.R: | ||
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| + Step1: load in gene expression datasets for network construction (exp-load) | ||
| + Step2: normalization for the exp dataset (exp-QC) | ||
| + Step3: check sample cluster info, optional (exp-cluster) | ||
| + Step4: prepare [SJARACNE](https://github.com/jyyulab/SJARACNe) (sjaracne-prep) | ||
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| ### Demo script for network-based analysis | ||
| Summary of steps in pipeline_analysis_demo1.R: | ||
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| + Step1: load in gene expression datasets for analysis (exp-load,exp-cluster,exp-QC) | ||
| + Step2: activity calculation (act-prep,act-get) | ||
| + Step3: get DE/DA (act-DA) | ||
| + Step4: generate master table (ms-tab) | ||
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| ### Demo script for the following analyses, mainly focus on visualization | ||
| Questions that the analyses in analysis_and_plot_demo1.R help to answer: | ||
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||
| + Part I: More details about the top drivers | ||
| 1. How to get the top drivers with significant differential activity (DA) in the comparison between G4 vs. other subtypes? | ||
| 2. How to interpret the significance of top DA drivers? | ||
| 3. What is the expression/activity pattern of these top DA drivers across sample subtypes? | ||
| 4. What are the biological functions of these top DA drivers? | ||
| 5. What are the biological functions of the target genes of these top DA drivers? | ||
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| + Part II: More details about the selected driver | ||
| 1. How to interpret the significance of the selected driver? | ||
| 2. How to visualize the network structure of the selected driver? | ||
| 3. What is the expression/activity of this selected driver across subtypes of sample? | ||
| 4. What are the functions of the target genes of this selected driver? | ||
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||
| + Part III: Other analyses | ||
| 1. What are the activities of the curated gene sets across all samples? | ||
| 2. How to find drivers share significantly overlapped target genes? | ||
|
|
||
| # NetBID 2.0 | ||
| NetBID (**Net**work-based **B**ayesian **I**nference of **D**rivers) is a data-driven system biology pipeline and toolkit for finding drivers from transcriptomics, proteomics and phosphoproteomics data, where the drivers can be either transcription factors (**TF**) or signaling factors (**SIG**). | ||
|
|
||
| NetBID 2.0 is an upgraded version of [NetBID 1.0](https://github.com/jyyulab/NetBID/releases/tag/1.0.0) that has been published in [Nature]((https://www.nature.com/articles/s41586-018-0177-0)) in 2018. NetBID 2.0 inherites all the main functions from NetBID 1.0, and provides many more functions and pipelines to perform advanced end-to-end analyses. | ||
|
|
||
| # Installation | ||
|
|
||
| Require ```R >= 3.6.0```. Other dependencies can be found in table [https://jyyulab.github.io/NetBID/docs/pre_request](https://jyyulab.github.io/NetBID/docs/pre_request). | ||
|
|
||
| Installation instructions are in [Installation section](https://jyyulab.github.io/NetBID/) of the documentation. | ||
|
|
||
|
|
||
| # Documentation & Guided Analyses | ||
|
|
||
| Instructions, documentation, and tutorials can be found at: | ||
|
|
||
| + [https://jyyulab.github.io/NetBID/](https://jyyulab.github.io/NetBID/) | ||
|
|
||
| A PDF manual [NetBID_manual.pdf](https://github.com/jyyulab/NetBID/blob/master/NetBID_manual.pdf) can be found in the repository. | ||
|
|
||
|
|
||
| # Docker | ||
| We publish our lastest docker builds on DockerHub. You can pull the docker image by running the following command: | ||
|
|
||
| ```$ docker pull adamdingliang/netbid2:2.0.1``` | ||
|
|
||
| The docker image has build-in RStudio server that can be launched by | ||
|
|
||
| ```$ docker run -it netbid2:2.0.1 rserver --server-daemonize 0``` | ||
|
|
||
| For interactive command line analysis, use the following command: | ||
|
|
||
| ```$ docker run -it netbid2:2.0.1``` | ||
|
|
||
| # Demos | ||
| Demo scripts can be found in [demo_scripts](https://github.com/jyyulab/NetBID/tree/master/demo_scripts) directory. | ||
|
|
||
| ### Demo script for network generation | ||
| Summary of steps in pipeline_network_demo1.R: | ||
|
|
||
| + Step1: load in gene expression datasets for network construction (exp-load) | ||
| + Step2: normalization for the exp dataset (exp-QC) | ||
| + Step3: check sample cluster info, optional (exp-cluster) | ||
| + Step4: prepare [SJARACNE](https://github.com/jyyulab/SJARACNe) (sjaracne-prep) | ||
|
|
||
| ### Demo script for network-based analysis | ||
| Summary of steps in pipeline_analysis_demo1.R: | ||
|
|
||
| + Step1: load in gene expression datasets for analysis (exp-load,exp-cluster,exp-QC) | ||
| + Step2: activity calculation (act-prep,act-get) | ||
| + Step3: get DE/DA (act-DA) | ||
| + Step4: generate master table (ms-tab) | ||
|
|
||
| ### Demo script for the following analyses, mainly focus on visualization | ||
| Questions that the analyses in analysis_and_plot_demo1.R help to answer: | ||
|
|
||
| + Part I: More details about the top drivers | ||
| 1. How to get the top drivers with significant differential activity (DA) in the comparison between G4 vs. other subtypes? | ||
| 2. How to interpret the significance of top DA drivers? | ||
| 3. What is the expression/activity pattern of these top DA drivers across sample subtypes? | ||
| 4. What are the biological functions of these top DA drivers? | ||
| 5. What are the biological functions of the target genes of these top DA drivers? | ||
|
|
||
| + Part II: More details about the selected driver | ||
| 1. How to interpret the significance of the selected driver? | ||
| 2. How to visualize the network structure of the selected driver? | ||
| 3. What is the expression/activity of this selected driver across subtypes of sample? | ||
| 4. What are the functions of the target genes of this selected driver? | ||
|
|
||
| + Part III: Other analyses | ||
| 1. What are the activities of the curated gene sets across all samples? | ||
| 2. How to find drivers share significantly overlapped target genes? | ||
| 3. How to draw oncoPrint figures for samples with different mutation information? | ||
|
|