diff --git a/.codeboarding/Command_Line_Interface_CLI_.md b/.codeboarding/Command_Line_Interface_CLI_.md
new file mode 100644
index 0000000000..026359d2b1
--- /dev/null
+++ b/.codeboarding/Command_Line_Interface_CLI_.md
@@ -0,0 +1,185 @@
+```mermaid
+
+graph LR
+
+ Command_Line_Interface_CLI_["Command-Line Interface (CLI)"]
+
+ Data_Input_Output_I_O_["Data Input/Output (I/O)"]
+
+ Core_Processing_Engine["Core Processing Engine"]
+
+ Data_Models_Utilities["Data Models & Utilities"]
+
+ Visualization_Layer["Visualization Layer"]
+
+ Configuration_Error_Handling["Configuration & Error Handling"]
+
+ Command_Line_Interface_CLI_ -- "Initiates Operations" --> Core_Processing_Engine
+
+ Command_Line_Interface_CLI_ -- "Directs Data Flow" --> Data_Input_Output_I_O_
+
+ Data_Input_Output_I_O_ -- "Provides Data To" --> Core_Processing_Engine
+
+ Core_Processing_Engine -- "Processes Data From" --> Data_Input_Output_I_O_
+
+ Core_Processing_Engine -- "Utilizes" --> Data_Models_Utilities
+
+ Data_Models_Utilities -- "Defines Structure For" --> Core_Processing_Engine
+
+ Visualization_Layer -- "Renders Data From" --> Core_Processing_Engine
+
+ Visualization_Layer -- "Outputs Via" --> Data_Input_Output_I_O_
+
+ Configuration_Error_Handling -- "Informs" --> Command_Line_Interface_CLI_
+
+ Configuration_Error_Handling -- "Influences" --> Core_Processing_Engine
+
+ click Command_Line_Interface_CLI_ href "https://github.com/deeptools/deeptools/blob/master/.codeboarding//Command_Line_Interface_CLI_.md" "Details"
+
+```
+
+
+
+[](https://github.com/CodeBoarding/GeneratedOnBoardings)[](https://www.codeboarding.org/demo)[](mailto:contact@codeboarding.org)
+
+
+
+## Details
+
+
+
+One paragraph explaining the functionality which is represented by this graph. What the main flow is and what is its purpose.
+
+
+
+### Command-Line Interface (CLI) [[Expand]](./Command_Line_Interface_CLI_.md)
+
+The user-facing layer that interprets commands, validates parameters, and orchestrates the execution of specific deeptools functionalities. It's the gateway for users to interact with the entire suite.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.parserCommon` (1:1)
+
+- `deeptools.bamCompare.main` (233:309)
+
+- `deeptools.plotHeatmap.main` (807:892)
+
+
+
+
+
+### Data Input/Output (I/O)
+
+Manages the reading and writing of various bioinformatics file formats (e.g., BAM, BigWig, BED, GTF). It abstracts the complexities of file handling and ensures data can be ingested and exported correctly.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.bamHandler.openBam` (46:102)
+
+- `deeptools.writeBedGraph_bam_and_bw.writeBedGraph_bam_and_bw` (1:1)
+
+
+
+
+
+### Core Processing Engine
+
+Contains the primary algorithms and computational logic for performing bioinformatics analyses, such as read counting, coverage calculation, data normalization, and statistical comparisons. This is where the core scientific computations occur.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.countReadsPerBin` (1:1)
+
+- `deeptools.bamCoverage` (1:1)
+
+- `deeptools.bamCompare` (1:1)
+
+- `deeptools.computeMatrix` (1:1)
+
+
+
+
+
+### Data Models & Utilities
+
+Defines standardized data structures for genomic intervals, read alignments, and coverage profiles, and provides a collection of general-purpose helper functions for common genomic operations, data manipulation, and statistical calculations.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.utilities` (1:1)
+
+
+
+
+
+### Visualization Layer
+
+Responsible for generating high-quality plots and visual representations of processed genomic data, such as heatmaps, profile plots, and coverage tracks. It transforms numerical results into interpretable graphical insights.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.plotHeatmap` (1:1)
+
+- `deeptools.plotProfile` (1:1)
+
+- `deeptools.heatmapper` (176:1058)
+
+
+
+
+
+### Configuration & Error Handling
+
+Manages application-wide settings, default parameters, and user-defined preferences, ensuring consistent behavior. It also centralizes error and exception handling to provide robust and informative feedback.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.utilities.get_config_args` (1:1)
+
+- `deeptools.utilities.SmartException` (1:1)
+
+
+
+
+
+
+
+
+
+### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)
\ No newline at end of file
diff --git a/.codeboarding/Core_Bioinformatics_Algorithms.md b/.codeboarding/Core_Bioinformatics_Algorithms.md
new file mode 100644
index 0000000000..69b49c74f6
--- /dev/null
+++ b/.codeboarding/Core_Bioinformatics_Algorithms.md
@@ -0,0 +1,245 @@
+```mermaid
+
+graph LR
+
+ Core_Bioinformatics_Algorithms["Core Bioinformatics Algorithms"]
+
+ BAM_BigWig_Data_Access["BAM/BigWig Data Access"]
+
+ Map_Reduce_Framework["Map-Reduce Framework"]
+
+ General_Utilities["General Utilities"]
+
+ CLI_Configuration["CLI & Configuration"]
+
+ Matrix_Generation["Matrix Generation"]
+
+ Matrix_Operations["Matrix Operations"]
+
+ Visualization_Layer["Visualization Layer"]
+
+ CLI_Configuration -- "configures" --> Core_Bioinformatics_Algorithms
+
+ CLI_Configuration -- "configures" --> BAM_BigWig_Data_Access
+
+ BAM_BigWig_Data_Access -- "provides data to" --> Core_Bioinformatics_Algorithms
+
+ Core_Bioinformatics_Algorithms -- "utilizes" --> Map_Reduce_Framework
+
+ Core_Bioinformatics_Algorithms -- "generates input for" --> Matrix_Generation
+
+ Matrix_Generation -- "produces input for" --> Matrix_Operations
+
+ Matrix_Operations -- "prepares data for" --> Visualization_Layer
+
+ Core_Bioinformatics_Algorithms -- "uses" --> General_Utilities
+
+ General_Utilities -- "supports" --> CLI_Configuration
+
+ General_Utilities -- "supports" --> BAM_BigWig_Data_Access
+
+ General_Utilities -- "supports" --> Map_Reduce_Framework
+
+ General_Utilities -- "supports" --> Matrix_Generation
+
+ General_Utilities -- "supports" --> Matrix_Operations
+
+ General_Utilities -- "supports" --> Visualization_Layer
+
+ click Core_Bioinformatics_Algorithms href "https://github.com/deeptools/deeptools/blob/master/.codeboarding//Core_Bioinformatics_Algorithms.md" "Details"
+
+```
+
+
+
+[](https://github.com/CodeBoarding/GeneratedOnBoardings)[](https://www.codeboarding.org/demo)[](mailto:contact@codeboarding.org)
+
+
+
+## Details
+
+
+
+Analysis of the `deeptools` package, focusing on its core components and their relationships. The `Core Bioinformatics Algorithms` component is central to `deeptools` as it encapsulates the fundamental computational logic for genomic data processing.
+
+
+
+### Core Bioinformatics Algorithms [[Expand]](./Core_Bioinformatics_Algorithms.md)
+
+This component is the computational engine, housing the fundamental algorithms for processing raw genomic data. It includes critical tasks such as counting reads per genomic bin, estimating fragment sizes, calculating coverage profiles, and applying essential normalization methods (e.g., GC content bias correction, scaling factors). These algorithms form the bedrock for all quantitative analyses performed by the suite.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.countReadsPerBin` (1:1)
+
+- `deeptools.getFragmentAndReadSize` (1:1)
+
+- `deeptools.sumCoveragePerBin` (1:1)
+
+- `deeptools.computeGCBias` (1:1)
+
+- `deeptools.correctGCBias` (1:1)
+
+- `deeptools.getScaleFactor` (1:1)
+
+- `deeptools.writeBedGraph` (1:1)
+
+- `deeptools.getRatio` (21:81)
+
+
+
+
+
+### BAM/BigWig Data Access
+
+Responsible for efficient reading and parsing of genomic data from standard bioinformatics file formats like BAM (for aligned reads) and BigWig (for pre-computed coverage tracks). This component handles the low-level I/O operations, ensuring data can be accessed quickly and reliably for downstream processing.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `pysam` (1:1)
+
+- `pyBigWig` (1:1)
+
+- `py2bit` (1:1)
+
+- `deeptools.utilities` (1:1)
+
+- `deeptools.io` (1:1)
+
+
+
+
+
+### Map-Reduce Framework
+
+Provides a scalable framework for distributing computational tasks across multiple cores or nodes, particularly for large genomic datasets. This enables parallel processing of genomic bins or regions, significantly speeding up analysis.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `multiprocessing` (1:1)
+
+- `deeptools.utilities` (1:1)
+
+
+
+
+
+### General Utilities
+
+A collection of helper functions and common utilities used across various components. This includes error handling, logging, file path manipulation, and other general-purpose functionalities that support the main algorithms and data processing pipelines.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.utilities` (1:1)
+
+
+
+
+
+### CLI & Configuration
+
+Manages command-line argument parsing, user input validation, and configuration file handling. This component provides the user interface for interacting with the `deeptools` suite, allowing users to specify parameters and control the execution of analyses.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.cli` (1:1)
+
+
+
+
+
+### Matrix Generation
+
+Responsible for taking processed genomic data (e.g., coverage profiles, read counts) and transforming it into a structured matrix format suitable for downstream analysis and visualization. This often involves creating heatmaps or profile plots.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.heatmapper._matrix` (1078:1371)
+
+
+
+
+
+### Matrix Operations
+
+Provides functionalities for manipulating and operating on the generated matrices. This could include normalization, aggregation, clustering, or other statistical transformations applied to the data matrices before visualization or further analysis.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.heatmapper` (176:1058)
+
+
+
+
+
+### Visualization Layer
+
+Handles the generation of various plots and visualizations (e.g., heatmaps, profile plots, scatter plots) from the processed and transformed data. This component leverages libraries like `matplotlib` and `plotly` to create informative graphical representations of the genomic data.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `matplotlib` (1:1)
+
+- `plotly` (1:1)
+
+- `deeptools.plotProfile` (1:1)
+
+- `deeptools.plotHeatmap` (1:1)
+
+
+
+
+
+
+
+
+
+### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)
\ No newline at end of file
diff --git a/.codeboarding/Data_I_O_Management.md b/.codeboarding/Data_I_O_Management.md
new file mode 100644
index 0000000000..6c1d096747
--- /dev/null
+++ b/.codeboarding/Data_I_O_Management.md
@@ -0,0 +1,101 @@
+```mermaid
+
+graph LR
+
+ Genomic_File_I_O["Genomic File I/O"]
+
+ Matrix_Data_Model_Persistence["Matrix Data Model & Persistence"]
+
+ Matrix_Generation_Transformation["Matrix Generation & Transformation"]
+
+ Matrix_Generation_Transformation -- "relies on" --> Genomic_File_I_O
+
+ Matrix_Generation_Transformation -- "utilizes" --> Matrix_Data_Model_Persistence
+
+ Genomic_File_I_O -- "feeds data to" --> Matrix_Generation_Transformation
+
+```
+
+
+
+[](https://github.com/CodeBoarding/GeneratedOnBoardings)[](https://www.codeboarding.org/demo)[](mailto:contact@codeboarding.org)
+
+
+
+## Details
+
+
+
+Rationale for changes: 1. Validation of _matrix data model: The _matrix class in deeptools/heatmapper.py (lines 1078-1371) was analyzed. It clearly defines the structure for holding heatmapper matrices, including the main data array (self.matrix), genomic regions, and boundaries for sample and group divisions. It also provides methods for accessing sub-matrices and managing labels, confirming its role as the core data model for the Matrix Data Model & Persistence component. 2. Control flow and method invocation analysis for deeptools.computeMatrix and deeptools.computeMatrixOperations: deeptools.computeMatrix was found to interact with Genomic File I/O by calling deeptools.bamHandler for reading genomic data and with Matrix Data Model & Persistence by calling deeptools.heatmapper.save_matrix to persist the generated matrix. deeptools.computeMatrixOperations was found to interact with Matrix Data Model & Persistence by calling deeptools.heatmapper.read_matrix_file to load existing matrices for further processing and deeptools.heatmapper.save_matrix to save the modified matrices. The descriptions of Matrix Generation & Transformation and Matrix Data Model & Persistence have been updated to reflect these explicit interactions. 3. Removal of redundant relationship: As per the feedback, the relationship "(Matrix Data Model & Persistence, provides data to, Matrix Generation & Transformation)" has been removed. The "utilizes" relationship adequately covers the interaction where Matrix Generation & Transformation uses Matrix Data Model & Persistence for storing and managing matrices, and the specific data provision for operations on existing matrices is now implicitly covered by the detailed description of computeMatrixOperations's interaction with read_matrix_file.
+
+
+
+### Genomic File I/O
+
+This component provides the foundational layer for interacting with raw genomic data files, specifically BAM/SAM alignment files and BigWig/BedGraph coverage files. Its core responsibility is to abstract the complexities of file parsing and data retrieval, offering functionalities for opening files, extracting basic mapping statistics, and efficiently fetching region-specific data. It also handles the writing of processed data back into standard formats like BedGraph.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.bamHandler` (1:1)
+
+- `deeptools.writeBedGraph` (1:1)
+
+- `deeptools.writeBedGraph_bam_and_bw` (1:1)
+
+
+
+
+
+### Matrix Data Model & Persistence
+
+This component is dedicated to defining the internal structure and managing the persistence of the structured data matrices that are central to many deeptools analyses, particularly for heatmap generation and other quantitative visualizations. It encompasses the internal data representation (e.g., metadata, sample information, actual signal values) and the mechanisms for reading these matrices from and writing them to disk (often compressed, e.g., .gz files). The _matrix class serves as the core data model, holding the main matrix data, genomic regions, and boundaries for sample and group divisions, along with methods for accessing and managing sub-matrices.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.heatmapper._matrix` (1078:1371)
+
+- `deeptools.heatmapper.heatmapper.read_matrix_file` (751:811)
+
+- `deeptools.heatmapper.heatmapper.save_matrix` (813:871)
+
+
+
+
+
+### Matrix Generation & Transformation
+
+This component is responsible for the computational processes that transform raw genomic data (accessed via the Genomic File I/O component) into the structured matrices managed by the Matrix Data Model & Persistence component. It includes the logic for calculating coverage, normalizing signals, and applying various transformations (e.g., binning, scaling) to prepare data for downstream analysis, such as heatmaps and profile plots. deeptools.computeMatrix orchestrates the initial matrix generation, interacting with Genomic File I/O to read data and Matrix Data Model & Persistence to save the resulting matrix. deeptools.computeMatrixOperations handles further transformations and manipulations of existing matrices, potentially reading them from and writing them back to the Matrix Data Model & Persistence component.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.computeMatrix` (1:1)
+
+- `deeptools.computeMatrixOperations` (1:1)
+
+
+
+
+
+
+
+
+
+### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)
\ No newline at end of file
diff --git a/.codeboarding/Parallel_Execution_Engine.md b/.codeboarding/Parallel_Execution_Engine.md
new file mode 100644
index 0000000000..b3259a9d16
--- /dev/null
+++ b/.codeboarding/Parallel_Execution_Engine.md
@@ -0,0 +1,131 @@
+```mermaid
+
+graph LR
+
+ Parallel_Execution_Engine["Parallel Execution Engine"]
+
+ Core_Bioinformatics_Algorithms["Core Bioinformatics Algorithms"]
+
+ Data_I_O_Management["Data I/O & Management"]
+
+ Tool_Workflow_Orchestrator_CLI_Interface_["Tool Workflow Orchestrator (CLI Interface)"]
+
+ Core_Bioinformatics_Algorithms -- "relies on" --> Parallel_Execution_Engine
+
+ Data_I_O_Management -- "provides data to" --> Parallel_Execution_Engine
+
+ Tool_Workflow_Orchestrator_CLI_Interface_ -- "configures" --> Parallel_Execution_Engine
+
+ Tool_Workflow_Orchestrator_CLI_Interface_ -- "uses" --> Core_Bioinformatics_Algorithms
+
+ Core_Bioinformatics_Algorithms -- "uses" --> Data_I_O_Management
+
+ Tool_Workflow_Orchestrator_CLI_Interface_ -- "uses" --> Data_I_O_Management
+
+ click Parallel_Execution_Engine href "https://github.com/deeptools/deeptools/blob/master/.codeboarding//Parallel_Execution_Engine.md" "Details"
+
+ click Core_Bioinformatics_Algorithms href "https://github.com/deeptools/deeptools/blob/master/.codeboarding//Core_Bioinformatics_Algorithms.md" "Details"
+
+ click Data_I_O_Management href "https://github.com/deeptools/deeptools/blob/master/.codeboarding//Data_I_O_Management.md" "Details"
+
+```
+
+
+
+[](https://github.com/CodeBoarding/GeneratedOnBoardings)[](https://www.codeboarding.org/demo)[](mailto:contact@codeboarding.org)
+
+
+
+## Details
+
+
+
+An updated analysis of the `deeptools` package, detailing its abstract components and their relationships, with a focus on specific source code references. Note: Specific line numbers for source code references were not provided and have been defaulted to 1 for both start and end lines. File paths are inferred from qualified names (e.g., `deeptools.module` becomes `deeptools/module.py`).
+
+
+
+### Parallel Execution Engine [[Expand]](./Parallel_Execution_Engine.md)
+
+The Parallel Execution Engine provides a robust framework for distributing and executing computationally intensive tasks across multiple processes or threads, leveraging a MapReduce-like paradigm for efficiency. It abstracts the complexities of parallelization, enabling other components to perform large-scale genomic data processing. This component is crucial for handling the large datasets typical in genomics, significantly reducing processing times.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.mapReduce` (7:152)
+
+
+
+
+
+### Core Bioinformatics Algorithms [[Expand]](./Core_Bioinformatics_Algorithms.md)
+
+This component encapsulates the core algorithms for various bioinformatics tasks, such as read counting, coverage calculation, and matrix generation. These algorithms are often computationally intensive and leverage the `Parallel Execution Engine` for efficient processing of large genomic datasets.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.countReadsPerBin` (1:1)
+
+- `deeptools.bamCoverage` (1:1)
+
+- `deeptools.computeMatrix` (1:1)
+
+
+
+
+
+### Data I/O & Management [[Expand]](./Data_I_O_Management.md)
+
+This component handles the input and output of data, including reading and writing various genomic file formats (e.g., BAM, BigWig, BED) and managing data structures within the `deeptools` suite. It provides the necessary interfaces for other components to access and persist genomic data.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.bamHandler` (1:1)
+
+- `deeptools.writeBedGraph` (1:1)
+
+
+
+
+
+### Tool Workflow Orchestrator (CLI Interface)
+
+This component manages the overall workflow of the `deeptools` suite, primarily through a command-line interface. It handles argument parsing, validation, and orchestrates the execution of various bioinformatics tools by configuring and invoking the `Core Bioinformatics Algorithms` and leveraging the `Parallel Execution Engine` and `Data I/O & Management` components.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.parserCommon` (1:1)
+
+- `deeptools.deeptools_list_tools` (1:1)
+
+
+
+
+
+
+
+
+
+### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)
\ No newline at end of file
diff --git a/.codeboarding/Tool_Workflow_Orchestrator.md b/.codeboarding/Tool_Workflow_Orchestrator.md
new file mode 100644
index 0000000000..7372d795cd
--- /dev/null
+++ b/.codeboarding/Tool_Workflow_Orchestrator.md
@@ -0,0 +1,307 @@
+```mermaid
+
+graph LR
+
+ CLI_Tools_Tool_Workflow_Orchestrator_["CLI Tools (Tool Workflow Orchestrator)"]
+
+ Argument_Parsing_Common_Utilities["Argument Parsing & Common Utilities"]
+
+ Data_I_O_Management_BAM_CRAM_BigWig_["Data I/O & Management (BAM/CRAM/BigWig)"]
+
+ Core_Bioinformatics_Algorithms_Read_Quantification_["Core Bioinformatics Algorithms (Read Quantification)"]
+
+ Data_Matrix_Generation["Data Matrix Generation"]
+
+ Data_Output_BedGraph_BigWig_Writer_["Data Output (BedGraph/BigWig Writer)"]
+
+ Parallel_Processing_Framework["Parallel Processing Framework"]
+
+ Visualization_Engine["Visualization Engine"]
+
+ CLI_Tools_Tool_Workflow_Orchestrator_ -- "uses" --> Argument_Parsing_Common_Utilities
+
+ CLI_Tools_Tool_Workflow_Orchestrator_ -- "uses" --> Data_I_O_Management_BAM_CRAM_BigWig_
+
+ CLI_Tools_Tool_Workflow_Orchestrator_ -- "uses" --> Core_Bioinformatics_Algorithms_Read_Quantification_
+
+ CLI_Tools_Tool_Workflow_Orchestrator_ -- "uses" --> Data_Matrix_Generation
+
+ CLI_Tools_Tool_Workflow_Orchestrator_ -- "uses" --> Data_Output_BedGraph_BigWig_Writer_
+
+ CLI_Tools_Tool_Workflow_Orchestrator_ -- "uses" --> Parallel_Processing_Framework
+
+ CLI_Tools_Tool_Workflow_Orchestrator_ -- "uses" --> Visualization_Engine
+
+ Core_Bioinformatics_Algorithms_Read_Quantification_ -- "uses" --> Data_I_O_Management_BAM_CRAM_BigWig_
+
+ Core_Bioinformatics_Algorithms_Read_Quantification_ -- "uses" --> Argument_Parsing_Common_Utilities
+
+ Core_Bioinformatics_Algorithms_Read_Quantification_ -- "uses" --> Parallel_Processing_Framework
+
+ Data_Matrix_Generation -- "uses" --> Core_Bioinformatics_Algorithms_Read_Quantification_
+
+ Data_Matrix_Generation -- "uses" --> Data_I_O_Management_BAM_CRAM_BigWig_
+
+ Data_Matrix_Generation -- "uses" --> Argument_Parsing_Common_Utilities
+
+ Data_Matrix_Generation -- "uses" --> Parallel_Processing_Framework
+
+ Data_Output_BedGraph_BigWig_Writer_ -- "uses" --> Core_Bioinformatics_Algorithms_Read_Quantification_
+
+ Data_Output_BedGraph_BigWig_Writer_ -- "uses" --> Argument_Parsing_Common_Utilities
+
+ Visualization_Engine -- "uses" --> Data_Matrix_Generation
+
+ Visualization_Engine -- "uses" --> Argument_Parsing_Common_Utilities
+
+ Parallel_Processing_Framework -- "uses" --> Argument_Parsing_Common_Utilities
+
+ Data_I_O_Management_BAM_CRAM_BigWig_ -- "uses" --> Argument_Parsing_Common_Utilities
+
+ click Visualization_Engine href "https://github.com/deeptools/deeptools/blob/master/.codeboarding//Visualization_Engine.md" "Details"
+
+```
+
+
+
+[](https://github.com/CodeBoarding/GeneratedOnBoardings)[](https://www.codeboarding.org/demo)[](mailto:contact@codeboarding.org)
+
+
+
+## Details
+
+
+
+The Tool Workflow Orchestrator component in deeptools serves as the high-level control layer for each specific command-line tool. It acts as the central coordinator, integrating various core functionalities to execute a complete bioinformatics workflow from start to finish.
+
+
+
+### CLI Tools (Tool Workflow Orchestrator)
+
+These are the user-facing entry points for each deeptools command. They orchestrate the entire workflow by parsing arguments, calling core bioinformatics algorithms, managing data I/O, and initiating visualization or output. They are fundamental as they provide the high-level logic and integration necessary for users to execute complex bioinformatics tasks.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.alignmentSieve` (1:1)
+
+- `deeptools.bamCompare` (1:1)
+
+- `deeptools.bamCoverage` (1:1)
+
+- `deeptools.multiBamSummary` (1:1)
+
+- `deeptools.bigwigCompare` (1:1)
+
+- `deeptools.bamPEFragmentSize` (1:1)
+
+- `deeptools.computeGCBias` (1:1)
+
+- `deeptools.computeMatrix` (1:1)
+
+- `deeptools.correctGCBias` (1:1)
+
+- `deeptools.estimateReadFiltering` (1:1)
+
+- `deeptools.estimateScaleFactor` (1:1)
+
+- `deeptools.plotCorrelation` (1:1)
+
+- `deeptools.plotCoverage` (1:1)
+
+- `deeptools.plotEnrichment` (358:451)
+
+- `deeptools.plotFingerprint` (1:1)
+
+- `deeptools.plotHeatmap` (1:1)
+
+- `deeptools.plotPCA` (1:1)
+
+- `deeptools.plotProfile` (1:1)
+
+- `deeptools.bigwigAverage` (1:1)
+
+- `deeptools.multiBigwigSummary` (1:1)
+
+
+
+
+
+### Argument Parsing & Common Utilities
+
+Centralizes the definition and parsing of command-line arguments, ensuring consistency across tools. It also includes general-purpose helper functions for tasks like temporary file management, label generation, and common data structures, promoting code reusability. This is fundamental for a robust and user-friendly interface and maintaining a clean codebase.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.parserCommon` (1:1)
+
+- `deeptools.utilities` (1:1)
+
+- `deeptools.cm` (1:1)
+
+- `deeptools.misc` (1:1)
+
+
+
+
+
+### Data I/O & Management (BAM/CRAM/BigWig)
+
+Handles the reading and management of primary genomic data formats (BAM/CRAM alignment files, BigWig/BedGraph coverage files). It acts as an abstraction layer for pysam and pyBigWig, crucial for efficient and standardized data access. This is fundamental for handling the diverse input data formats in genomics.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.bamHandler` (1:1)
+
+- `deeptools.getScorePerBigWigBin` (1:1)
+
+
+
+
+
+### Core Bioinformatics Algorithms (Read Quantification)
+
+Implements the core logic for quantifying sequencing reads within genomic regions or bins, including various counting strategies and normalization methods. This forms the analytical foundation for coverage, summary, and differential analyses. It's fundamental as it provides the basic quantitative measures for most bioinformatics analyses.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.countReadsPerBin` (1:1)
+
+- `deeptools.sumCoveragePerBin` (1:1)
+
+- `deeptools.getScaleFactor` (1:1)
+
+- `deeptools.SES_scaleFactor` (1:1)
+
+- `deeptools.getRatio` (21:81)
+
+- `deeptools.getFragmentAndReadSize` (1:1)
+
+
+
+
+
+### Data Matrix Generation
+
+Focuses on processing genomic data (e.g., read counts, coverage) into structured matrices suitable for downstream analysis and visualization, particularly for heatmaps and profiles. This component often involves complex aggregation and transformation logic. It's fundamental for preparing data for advanced visualization and comparative analysis.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.computeMatrix` (1:1)
+
+- `deeptools.computeMatrixOperations` (1:1)
+
+
+
+
+
+### Data Output (BedGraph/BigWig Writer)
+
+Responsible for writing processed genomic data into standard BedGraph and BigWig file formats, ensuring interoperability with other bioinformatics tools and visualization platforms. This is fundamental for persisting results and enabling further analysis.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.writeBedGraph` (1:1)
+
+- `deeptools.writeBedGraph_bam_and_bw` (1:1)
+
+
+
+
+
+### Parallel Processing Framework
+
+Provides a generic MapReduce-like framework for parallelizing computationally intensive data processing tasks, essential for efficiently handling large genomic datasets. This is fundamental for performance and scalability in scientific computing.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.mapReduce` (7:152)
+
+
+
+
+
+### Visualization Engine [[Expand]](./Visualization_Engine.md)
+
+Generates various plots and visualizations (e.g., heatmaps, profiles, correlations, PCA) from processed genomic data, leveraging libraries like matplotlib and plotly. This is fundamental for data interpretation, quality control, and presenting results.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.heatmapper` (176:1058)
+
+- `deeptools.heatmapper_utilities` (1:1)
+
+- `deeptools.plotCorrelation` (1:1)
+
+- `deeptools.plotCoverage` (1:1)
+
+- `deeptools.plotEnrichment` (358:451)
+
+- `deeptools.plotFingerprint` (1:1)
+
+- `deeptools.plotHeatmap` (1:1)
+
+- `deeptools.plotPCA` (1:1)
+
+- `deeptools.plotProfile` (1:1)
+
+- `deeptools.correlation` (1:1)
+
+- `deeptools.correlation_heatmap` (1:1)
+
+
+
+
+
+
+
+
+
+### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)
\ No newline at end of file
diff --git a/.codeboarding/Utilities.md b/.codeboarding/Utilities.md
new file mode 100644
index 0000000000..6102684ffb
--- /dev/null
+++ b/.codeboarding/Utilities.md
@@ -0,0 +1,391 @@
+```mermaid
+
+graph LR
+
+ deeptools_utilities["deeptools.utilities"]
+
+ deeptools_bamHandler["deeptools.bamHandler"]
+
+ deeptools_cm["deeptools.cm"]
+
+ deeptools_alignmentSieve["deeptools.alignmentSieve"]
+
+ deeptools_bamCompare["deeptools.bamCompare"]
+
+ deeptools_bamCoverage["deeptools.bamCoverage"]
+
+ deeptools_computeGCBias["deeptools.computeGCBias"]
+
+ deeptools_correctGCBias["deeptools.correctGCBias"]
+
+ deeptools_countReadsPerBin["deeptools.countReadsPerBin"]
+
+ deeptools_estimateReadFiltering["deeptools.estimateReadFiltering"]
+
+ deeptools_getScaleFactor["deeptools.getScaleFactor"]
+
+ deeptools_getScorePerBigWigBin["deeptools.getScorePerBigWigBin"]
+
+ deeptools_heatmapper["deeptools.heatmapper"]
+
+ deeptools_multiBamSummary["deeptools.multiBamSummary"]
+
+ deeptools_multiBigwigSummary["deeptools.multiBigwigSummary"]
+
+ deeptools_plotCoverage["deeptools.plotCoverage"]
+
+ deeptools_plotEnrichment["deeptools.plotEnrichment"]
+
+ deeptools_plotFingerprint["deeptools.plotFingerprint"]
+
+ deeptools_plotHeatmap["deeptools.plotHeatmap"]
+
+ deeptools_sumCoveragePerBin["deeptools.sumCoveragePerBin"]
+
+ deeptools_writeBedGraph["deeptools.writeBedGraph"]
+
+ deeptools_writeBedGraph_bam_and_bw["deeptools.writeBedGraph_bam_and_bw"]
+
+ deeptools_utilities -- "uses" --> deeptools_bamHandler
+
+ deeptools_utilities -- "uses" --> deeptools_cm
+
+ deeptools_alignmentSieve -- "uses" --> deeptools_utilities
+
+ deeptools_bamCompare -- "uses" --> deeptools_utilities
+
+ deeptools_bamCoverage -- "uses" --> deeptools_utilities
+
+ deeptools_computeGCBias -- "uses" --> deeptools_utilities
+
+ deeptools_correctGCBias -- "uses" --> deeptools_utilities
+
+ deeptools_countReadsPerBin -- "uses" --> deeptools_utilities
+
+ deeptools_estimateReadFiltering -- "uses" --> deeptools_utilities
+
+ deeptools_getScaleFactor -- "uses" --> deeptools_utilities
+
+ deeptools_getScorePerBigWigBin -- "uses" --> deeptools_utilities
+
+ deeptools_heatmapper -- "uses" --> deeptools_utilities
+
+ deeptools_multiBamSummary -- "uses" --> deeptools_utilities
+
+ deeptools_multiBigwigSummary -- "uses" --> deeptools_utilities
+
+ deeptools_plotCoverage -- "uses" --> deeptools_utilities
+
+ deeptools_plotEnrichment -- "uses" --> deeptools_utilities
+
+ deeptools_plotFingerprint -- "uses" --> deeptools_utilities
+
+ deeptools_plotHeatmap -- "uses" --> deeptools_utilities
+
+ deeptools_sumCoveragePerBin -- "uses" --> deeptools_utilities
+
+ deeptools_writeBedGraph -- "uses" --> deeptools_utilities
+
+ deeptools_writeBedGraph_bam_and_bw -- "uses" --> deeptools_utilities
+
+```
+
+
+
+[](https://github.com/CodeBoarding/GeneratedOnBoardings)[](https://www.codeboarding.org/demo)[](mailto:contact@codeboarding.org)
+
+
+
+## Details
+
+
+
+The `deeptools.utilities` component is fundamental because it embodies the principles of modular design and reusability, which are critical for a Scientific Computing/Bioinformatics Tool Suite. By centralizing common helper functions, it: 1. Reduces Code Duplication: Prevents the same logic from being rewritten across multiple modules, leading to a more concise and maintainable codebase. 2. Ensures Consistency: Standardizes operations like chromosome naming and data type conversions, which is crucial for data integrity and interoperability in bioinformatics. 3. Simplifies Development: Provides a readily available set of tools for developers, allowing them to focus on the core logic of new features rather than reimplementing basic functionalities. 4. Improves Maintainability: Changes or bug fixes to a utility function only need to be applied in one place, benefiting all components that use it. 5. Enhances Readability: Code that leverages well-named utility functions is generally easier to understand and follow. In essence, `deeptools.utilities` acts as the backbone for many operations within the `deeptools` project, making it an indispensable component for the overall architecture and functionality of the tool suite.
+
+
+
+### deeptools.utilities
+
+This component provides a comprehensive set of utility functions essential for various operations within `deeptools`. These utilities range from basic file I/O and string/byte conversions to more specialized bioinformatics tasks like chromosome name standardization and handling blacklisted reads in sequencing data. It acts as a support layer, ensuring common functionalities are centralized and consistently applied throughout the project.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.utilities:toString` (281:293)
+
+- `deeptools.utilities:toBytes` (296:308)
+
+- `deeptools.utilities:copyFileInMemory` (231:246)
+
+- `deeptools.utilities:getCommonChrNames` (160:228)
+
+- `deeptools.utilities:bam_blacklisted_worker` (345:355)
+
+- `deeptools.utilities:smartLabels` (27:28)
+
+
+
+
+
+### deeptools.bamHandler
+
+Handles core BAM file operations.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### deeptools.cm
+
+Provides functionalities related to colormaps or visual elements.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### deeptools.alignmentSieve
+
+A component within the deeptools project.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### deeptools.bamCompare
+
+A component within the deeptools project.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### deeptools.bamCoverage
+
+A component within the deeptools project.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### deeptools.computeGCBias
+
+A component within the deeptools project.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### deeptools.correctGCBias
+
+A component within the deeptools project.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### deeptools.countReadsPerBin
+
+A component within the deeptools project.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### deeptools.estimateReadFiltering
+
+A component within the deeptools project.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### deeptools.getScaleFactor
+
+A component within the deeptools project.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### deeptools.getScorePerBigWigBin
+
+A component within the deeptools project.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### deeptools.heatmapper
+
+A component within the deeptools project.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### deeptools.multiBamSummary
+
+A component within the deeptools project.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### deeptools.multiBigwigSummary
+
+A component within the deeptools project.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### deeptools.plotCoverage
+
+A component within the deeptools project.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### deeptools.plotEnrichment
+
+A component within the deeptools project.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### deeptools.plotFingerprint
+
+A component within the deeptools project.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### deeptools.plotHeatmap
+
+A component within the deeptools project.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### deeptools.sumCoveragePerBin
+
+A component within the deeptools project.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### deeptools.writeBedGraph
+
+A component within the deeptools project.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### deeptools.writeBedGraph_bam_and_bw
+
+A component within the deeptools project.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+
+
+
+
+### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)
\ No newline at end of file
diff --git a/.codeboarding/Visualization_Engine.md b/.codeboarding/Visualization_Engine.md
new file mode 100644
index 0000000000..958d22f73f
--- /dev/null
+++ b/.codeboarding/Visualization_Engine.md
@@ -0,0 +1,227 @@
+```mermaid
+
+graph LR
+
+ Visualization_Engine["Visualization Engine"]
+
+ deeptools_plotCorrelation["deeptools.plotCorrelation"]
+
+ deeptools_plotCoverage["deeptools.plotCoverage"]
+
+ deeptools_plotHeatmap["deeptools.plotHeatmap"]
+
+ deeptools_plotProfile["deeptools.plotProfile"]
+
+ deeptools_plotPCA["deeptools.plotPCA"]
+
+ deeptools_heatmapper["deeptools.heatmapper"]
+
+ deeptools_heatmapper_utilities["deeptools.heatmapper_utilities"]
+
+ deeptools_cm["deeptools.cm"]
+
+ Visualization_Engine -- "consumes data from" --> Matrix_I_O_Internal_Representation
+
+ Visualization_Engine -- "is configured by" --> CLI_Configuration
+
+ Visualization_Engine -- "utilizes" --> General_Utilities
+
+ deeptools_plotHeatmap -- "depends on" --> deeptools_heatmapper
+
+ deeptools_plotHeatmap -- "depends on" --> deeptools_heatmapper_utilities
+
+ deeptools_plotProfile -- "depends on" --> deeptools_heatmapper
+
+ deeptools_plotProfile -- "depends on" --> deeptools_heatmapper_utilities
+
+ deeptools_plotCorrelation -- "depends on" --> deeptools_cm
+
+ deeptools_plotCoverage -- "depends on" --> deeptools_cm
+
+ deeptools_plotHeatmap -- "depends on" --> deeptools_cm
+
+ deeptools_plotProfile -- "depends on" --> deeptools_cm
+
+ deeptools_plotPCA -- "depends on" --> deeptools_cm
+
+ deeptools_heatmapper_utilities -- "depends on" --> deeptools_cm
+
+ click Visualization_Engine href "https://github.com/deeptools/deeptools/blob/master/.codeboarding//Visualization_Engine.md" "Details"
+
+```
+
+
+
+[](https://github.com/CodeBoarding/GeneratedOnBoardings)[](https://www.codeboarding.org/demo)[](mailto:contact@codeboarding.org)
+
+
+
+## Details
+
+
+
+Analysis of the 'Visualization Engine' in 'deeptools', detailing its structure, core modules, and inter-component relationships for generating diverse graphical representations from processed genomic data.
+
+
+
+### Visualization Engine [[Expand]](./Visualization_Engine.md)
+
+This component is dedicated to the generation of diverse graphical representations from processed genomic data and analysis results. It encompasses functionalities for creating heatmaps, profile plots, scatter plots, and PCA plots. It acts as the primary interface for transforming numerical data into insightful visual outputs, relying on internal data structures (matrices) and external plotting libraries like Matplotlib and Plotly.
+
+
+
+
+
+**Related Classes/Methods**: _None_
+
+
+
+### deeptools.plotCorrelation
+
+Handles the generation of correlation plots, visualizing the relationships between different genomic datasets.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.plotCorrelation` (1:1)
+
+
+
+
+
+### deeptools.plotCoverage
+
+Manages the creation of coverage plots, illustrating the sequencing depth across genomic regions.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.plotCoverage` (1:1)
+
+
+
+
+
+### deeptools.plotHeatmap
+
+Responsible for rendering heatmaps, which are essential for visualizing patterns in large-scale genomic data, such as gene expression or histone modification profiles.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.plotHeatmap` (1:1)
+
+
+
+
+
+### deeptools.plotProfile
+
+Generates profile plots, showing the average signal intensity across defined genomic regions.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.plotProfile` (1:1)
+
+
+
+
+
+### deeptools.plotPCA
+
+Creates PCA (Principal Component Analysis) plots, used for dimensionality reduction and visualizing sample relationships based on genomic features.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.plotPCA` (1:1)
+
+
+
+
+
+### deeptools.heatmapper
+
+A core module that manages the internal representation and processing of matrix data specifically for heatmap and profile plot generation. It includes functionalities for reading and saving matrix files and potentially the underlying plotting logic.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.heatmapper` (176:1058)
+
+
+
+
+
+### deeptools.heatmapper_utilities
+
+Provides utility functions that support the `heatmapper` module, likely for data manipulation or preparation specific to heatmap visualization.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.heatmapper_utilities` (1:1)
+
+
+
+
+
+### deeptools.cm
+
+This module appears to handle colormap definitions and related utilities, which are essential for the visual aesthetics and interpretability of plots.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.cm` (1:1)
+
+
+
+
+
+
+
+
+
+### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)
\ No newline at end of file
diff --git a/.codeboarding/on_boarding.md b/.codeboarding/on_boarding.md
new file mode 100644
index 0000000000..c23d2a5e4c
--- /dev/null
+++ b/.codeboarding/on_boarding.md
@@ -0,0 +1,265 @@
+```mermaid
+
+graph LR
+
+ Command_Line_Interface_CLI_["Command-Line Interface (CLI)"]
+
+ Data_I_O_Management["Data I/O & Management"]
+
+ Core_Bioinformatics_Algorithms["Core Bioinformatics Algorithms"]
+
+ Visualization_Engine["Visualization Engine"]
+
+ Tool_Workflow_Orchestrator["Tool Workflow Orchestrator"]
+
+ Parallel_Execution_Engine["Parallel Execution Engine"]
+
+ Utilities["Utilities"]
+
+ Command_Line_Interface_CLI_ -- "initiates workflows in" --> Tool_Workflow_Orchestrator
+
+ Data_I_O_Management -- "provides raw data to" --> Core_Bioinformatics_Algorithms
+
+ Core_Bioinformatics_Algorithms -- "sends processed data to" --> Data_I_O_Management
+
+ Data_I_O_Management -- "provides matrices/data to" --> Visualization_Engine
+
+ Tool_Workflow_Orchestrator -- "calls functions in" --> Data_I_O_Management
+
+ Core_Bioinformatics_Algorithms -- "receives raw data from" --> Data_I_O_Management
+
+ Core_Bioinformatics_Algorithms -- "provides processed data to" --> Visualization_Engine
+
+ Tool_Workflow_Orchestrator -- "receives data/matrices from" --> Data_I_O_Management
+
+ Command_Line_Interface_CLI_ -- "is initiated by" --> Tool_Workflow_Orchestrator
+
+ Tool_Workflow_Orchestrator -- "calls functions in" --> Data_I_O_Management
+
+ Tool_Workflow_Orchestrator -- "calls functions in" --> Core_Bioinformatics_Algorithms
+
+ Tool_Workflow_Orchestrator -- "calls functions in" --> Visualization_Engine
+
+ Parallel_Execution_Engine -- "is utilized by" --> Core_Bioinformatics_Algorithms
+
+ Parallel_Execution_Engine -- "is utilized by" --> Data_I_O_Management
+
+ Parallel_Execution_Engine -- "is utilized by" --> Tool_Workflow_Orchestrator
+
+ Utilities -- "supports" --> Command_Line_Interface_CLI_
+
+ Utilities -- "supports" --> Data_I_O_Management
+
+ Utilities -- "supports" --> Core_Bioinformatics_Algorithms
+
+ Utilities -- "supports" --> Visualization_Engine
+
+ Utilities -- "supports" --> Tool_Workflow_Orchestrator
+
+ Utilities -- "supports" --> Parallel_Execution_Engine
+
+ click Command_Line_Interface_CLI_ href "https://github.com/deeptools/deeptools/blob/master/.codeboarding//Command_Line_Interface_CLI_.md" "Details"
+
+ click Data_I_O_Management href "https://github.com/deeptools/deeptools/blob/master/.codeboarding//Data_I_O_Management.md" "Details"
+
+ click Core_Bioinformatics_Algorithms href "https://github.com/deeptools/deeptools/blob/master/.codeboarding//Core_Bioinformatics_Algorithms.md" "Details"
+
+ click Visualization_Engine href "https://github.com/deeptools/deeptools/blob/master/.codeboarding//Visualization_Engine.md" "Details"
+
+ click Tool_Workflow_Orchestrator href "https://github.com/deeptools/deeptools/blob/master/.codeboarding//Tool_Workflow_Orchestrator.md" "Details"
+
+ click Parallel_Execution_Engine href "https://github.com/deeptools/deeptools/blob/master/.codeboarding//Parallel_Execution_Engine.md" "Details"
+
+ click Utilities href "https://github.com/deeptools/deeptools/blob/master/.codeboarding//Utilities.md" "Details"
+
+```
+
+
+
+[](https://github.com/CodeBoarding/GeneratedOnBoardings)[](https://www.codeboarding.org/demo)[](mailto:contact@codeboarding.org)
+
+
+
+## Details
+
+
+
+The `deeptools` project is architected as a modular Scientific Computing / Bioinformatics Tool Suite, designed to process and visualize genomic data. Its architecture emphasizes a clear separation of concerns, enabling efficient data flow from command-line input through core processing to final visualization.
+
+
+
+### Command-Line Interface (CLI) [[Expand]](./Command_Line_Interface_CLI_.md)
+
+Serves as the primary entry point for users, responsible for parsing command-line arguments, validating inputs, and initiating the execution of specific `deeptools` tools. It translates user commands into internal workflow orchestrations.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.parserCommon` (1:10)
+
+- `deeptools.bamCompare.main` (233:309)
+
+- `deeptools.plotHeatmap.main` (807:892)
+
+
+
+
+
+### Data I/O & Management [[Expand]](./Data_I_O_Management.md)
+
+Handles all aspects of data ingress and egress, including reading from and writing to various bioinformatics file formats (BAM, BigWig, BedGraph, BED, GTF). It also manages the creation, manipulation, and storage of structured data matrices derived from genomic signals, which are central to many `deeptools` analyses.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.bamHandler` (1:10)
+
+- `deeptools.writeBedGraph` (1:10)
+
+- `deeptools.heatmapper.heatmapper.read_matrix_file` (751:811)
+
+- `deeptools.heatmapper.heatmapper.save_matrix` (813:871)
+
+- `deeptools.computeMatrix` (1:10)
+
+- `deeptools.computeMatrixOperations` (1:10)
+
+- `deeptools.heatmapper._matrix` (1078:1371)
+
+
+
+
+
+### Core Bioinformatics Algorithms [[Expand]](./Core_Bioinformatics_Algorithms.md)
+
+Encapsulates the fundamental algorithms for processing raw genomic data. This includes tasks such as counting reads per genomic bin, estimating fragment sizes, calculating coverage, and applying normalization methods (e.g., GC content bias correction, scaling factors). It performs the heavy computational lifting.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.countReadsPerBin.CountReadsPerBin` (30:960)
+
+- `deeptools.getFragmentAndReadSize` (1:10)
+
+- `deeptools.sumCoveragePerBin.SumCoveragePerBin` (9:213)
+
+- `deeptools.computeGCBias` (1:10)
+
+- `deeptools.correctGCBias` (1:10)
+
+- `deeptools.getScaleFactor` (1:10)
+
+
+
+
+
+### Visualization Engine [[Expand]](./Visualization_Engine.md)
+
+Responsible for rendering various plots and graphical representations of genomic data and analysis results. This includes heatmaps, profile plots, scatter plots, and PCA plots, leveraging libraries like Matplotlib and Plotly to create informative visual outputs.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.plotCorrelation` (1:10)
+
+- `deeptools.plotCoverage` (1:10)
+
+- `deeptools.plotHeatmap` (1:10)
+
+- `deeptools.plotProfile` (1:10)
+
+- `deeptools.plotPCA` (1:10)
+
+- `deeptools.heatmapper_utilities` (1:10)
+
+
+
+
+
+### Tool Workflow Orchestrator [[Expand]](./Tool_Workflow_Orchestrator.md)
+
+This layer defines the specific high-level logic for each `deeptools` command-line tool. It acts as the central coordinator, orchestrating calls between the `CLI` and the core functional components (`Data I/O & Management`, `Core Bioinformatics Algorithms`, `Visualization Engine`) to execute a complete bioinformatics workflow from start to finish.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.alignmentSieve` (1:10)
+
+- `deeptools.bamCompare` (1:10)
+
+- `deeptools.bamCoverage` (1:10)
+
+- `deeptools.multiBamSummary` (1:10)
+
+- `deeptools.bigwigCompare` (1:10)
+
+
+
+
+
+### Parallel Execution Engine [[Expand]](./Parallel_Execution_Engine.md)
+
+Provides a framework (`deeptools.mapReduce`) for distributing and executing computationally intensive tasks across multiple processes or threads, leveraging a MapReduce paradigm for efficiency. This service is utilized by the **Core Bioinformatics Algorithms**, **Data I/O & Management**, and **Tool Workflow Orchestrator** for performance optimization.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.mapReduce` (7:152)
+
+
+
+
+
+### Utilities [[Expand]](./Utilities.md)
+
+A collection of general-purpose helper functions (`deeptools.utilities`) used across various modules, including string conversions, file path handling, chromosome name standardization, and temporary file management. These utilities support almost all other components.
+
+
+
+
+
+**Related Classes/Methods**:
+
+
+
+- `deeptools.utilities` (1:10)
+
+
+
+
+
+
+
+
+
+### [FAQ](https://github.com/CodeBoarding/GeneratedOnBoardings/tree/main?tab=readme-ov-file#faq)
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