bitless/mirnapath2 repository overview

⁠Welcome to miRNAPath2 image

miRNAPathWeb provides a user-friendly access to miRNAPath2 (https://github.com/victor-ramos/miRNAPath2⁠).

⁠Getting Started

miRNAPAth2 aims to ease miRNA analysis in an integrative environment in which the users can perform the analysis using their own RNA-seq data. With miRNAPath2, it is possible to detect putative miRNA-mRNAs interactions in the analyzed system.

The user can run miRNAPath2 with input their own RNA-seq data or with the example data already avaible with miRNAPath2 such as Acute Myeloid Leukemia (TCGA-LAML), Stomach adenocarcinoma (TCGA-STAD) and Ovarian serous cystadenocarcinoma (TCGA-OV).

⁠Availability

miRNAPath2 is available in both ShinyApp and as an R package. For both, R package and ShinyApp, the input files must follow some patters, such as:

• File must have a header row.
• Expression data must be in TPM.
• File rownames must be gene identifiers.
• Input files must be from paired samples and of one type only, e.g. only cancer-type samples or only normal-type samples.

⁠ShinyApp

Code available on Github: https://github.com/victor-ramos/miRNAPathWeb⁠

⁠R Package

Code and manual available on Github: https://github.com/victor-ramos/miRNAPath2⁠

⁠Using miRNAPath2 Image

miRNAPathWeb is compatible with all operation systems as long as the user install one software named Docker.

⁠First Step, install Docker:

• Open up Docker webpage: https://docs.docker.com/install/⁠
• Windows users: Get Docker -> Docker CE -> Microsoft Windows
• Linux users: Get Docker -> Docker CE -> Linux
• MacOS users: Get Docker -> Docker CE -> MacOS

⁠Once Docker is installed, open a terminal window and let's go to the second step, download miRNAPath2 ShinyApp image:

• docker pull bitless/mirnapath2

⁠Third step, run miRNAPath2 docker:

• docker run -d --name=mirnapath2 --rm -p <ANY_AVAILABLE_PORT>:3838 bitless/mirnapath2

⁠Open up any web broswer you like, and type:

• http://localhost⁠:<THIRD_STEP_PORT>

⁠When you want to close de application, type:

• docker stop mirnapath2