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Update README.md
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SoloveyMaria authored Nov 8, 2023
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THE STRUCTURE SHOULD BE THE SAME AS IN ALL PREVIOUS DIRECTORIES. THAT IS IT SHOULD CONTAIN A GENERA TITLE AND SUBSECTIONS WITH THE DESCRIPTION OF SUBDIRECTORIES.

THIS SECTION CAN SERVE AS AN INTRO AFTER THE TITLE AND THE FURTHER SUBSECTIONS.
It is well recognized that communication tools and pipelines are limited by the data available in their respective LIGAND-RECEPTOR databases. Consequently, it is important to acknowledge that if the databases CONTAIN A bias TOWARDS A CERTAIN LIGAND-RECEPTOR SPECTRUM, so too are the results. Therefore, comparing default databases and creating unified custom databases is crucial to ensuring fair and accurate comparisons between different tools. -> THE LAST SENTENCE DOES NOT ADDRESS A PROBLEM STATED IN THE SETNECE BEFORE IT. I RATHER SUGGEST THAT AFTER MAKING A POINT ABOUT POTENTIAL BIAS (WHICH IS AN IMPORTANT ONE, BUT WE DO NOT ADDRESS IT IN OUR DATABASE EITHER), YOU ADD THE NEXT POINT ABOUT THE LIGANDRECEPTOR INTERACTIONS CONFIRMED IN THE LITERATURE VS INTERACTIONS BASED ON PREDICTIONS BY COMPUTATIONAL TOOLS ONLY. THEN SAY THAT DIFFERENT DATABASE INCLUDE THE LATTER TO DEFFERENT EXPENT, AND THEN SAY THAT IT IS WHAT WE COMPARE IN THE DATABASE COMPARISON SECTION.

(YOU DON'T START A NEW PARAGRAPH WITH "HOWEVER" OR ANY OTHER WORD THAT IS INTENDED TO GLUE A SENTENCE TO THE PREVIOUS ONE. AT THE BEGINNING OF A PARAGRAPH THERE IS NO "PREVIOUS SENTENCE" AND USAGE OF THESE WORDS MAKES AN IMPRESSION THAT YOU TORE APART A PIECE OF TEXT. REMOVE THIS WORD HERE AND START WITH "COMPARING") However, comparing databases can be challenging due to the diverse structures used by different tools. For instance, while `CellPhoneDB` utilizes `SQLAlchemy` with multiple tables, `community` uses a single table. ADD AN EXAMPLE OF WHAT NICHENET IS USING TO BE CONSISTENT. To simplify the process, we have designed the `community` tool in a user-friendly manner, enabling the creation of custom databases through spreadsheets or by exporting and modifying the default database as a csv/tsv file. -> IF THIS SECTION IS ONLY ABOUT THE COMMUNITY DATABASE AND HAS NOTHING ABOUT THE METHOD COMPARISON, THEN IT SHOULD BE IN THE COMMUNITY GITHUB AND NOT HERE. IF YOU WANT TO MAKE SOME MORE ELABORATED POINT ABOUT THE DIFFERENCES IN THE DATABASES, THEN GO INTO DETAILS HERE.

Notwithstanding, the process of building a custom database requires an in-depth understanding of the underlying biology and the specific experimental context. As such, it is essential to ensure that the database is well-curated and validated before using it for analysis. REMOVE THIS WHOLE PARAGRAPH -> IT HAS NO INFORMATION. PLUS, AGAIN, DON'T START PARAGRAPHS WITH "NONWITHSTANDING" ETC.

FROM HERE, START THE SUBSECTIONS. MAKE IT CLEARLY STRUCTURED, SHORT, PRESICE AND CONSISTENT. REMOVE ALL THE UNNECESSARY BLA-BLAING AROUND. MAKE SURE TO KEEP YOUR TEXT IN PASSIVE VOICE SUCH THAT IT IS CONSISTENT WITH THE PREVIOUS SECTIONS.

It is worth noting that the comparison of databases is facilitated through the [`/compare_databases`](./method_comparison/compare_algorithms) section of this directory, where default databases of `CellPhoneDB`, `NicheNet` and `community` can be compared. In contrast, the [/compare_algorithms/ section](./method_comparison/compare_algorithms) provides detailed instructions on how to generate a unified custom database for each tool. This approach aims to simplify the process of creating custom databases and enables users to easily modify the database to suit their specific experimental requirements.

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