(Para) Pathology Notes
  • Preface
  • Introduction
    • Introduction
    • GitBook Manual
    • Patoloji Notları
    • Patoloji Atlası
    • Edit Here
    • Pathology Pages
  • Medical School Lectures
    • Medical School Lectures
      • About Pathology Lectures
    • General Pathology
      • General Pathology Links
      • Introduction to Pathology
      • Cellular Pathology
      • Chronic Inflammation
      • Wound Healing
      • The Mechanisms of Cell Death, Apoptosis, and Autophagy
      • Intracellular Accumulations and Cellular Aging
      • Pathology of Infectious Diseases
      • Amyloidosis
    • Laboratory Lectures
      • Lab: Pathology of Heart and Vascular Diseases
      • Lab: Glomerular Diseases
      • Lab: Pathology of Breast
      • Lab: Pathology of Endocrine System-1
      • Lab: Pathology of Endocrine System-2
      • Lab: Pathology of Gastrointestinal Tract-2
      • Lab: Basic Tumor Pathology-1
      • Lab: Basic Tumor Pathology-2
      • Lab: Diseases and Tumors of Respiratory System-1
      • Lab: Gynecologic pathologies
      • Lab: Diseases and Tumors of Respiratory System-2
      • Lab: Infectious agents in tissues
      • Lab: Pathology of Gastrointestinal Tract-1
      • Lab Acute and Chronic Inflammation
      • Lab Cellular Injury
      • Lab Hemodynamic Disorders
      • Lab: Pathology of CNS
    • Public Health
    • Infectious Diseases
      • Vaccination
      • Fungal Diseases
      • Parasitic Diseases
  • Systemic Pathology
    • Systemic Pathology
    • Endocrine Pathology
    • Gastrointestinal Pathology
      • Esophagus Pathology
      • Stomach
      • Duodenal Biopsy
      • Polyps
      • Colon and Rectum
        • Colon Colorectal Carcinoma
        • Malignant Colorectal Polyps
    • Neuropathology
      • Injury in central nervous system and cerebrovascular diseases
      • Gliomlar
    • Bone and Soft Tissue
      • Yumuşak doku tümörleri
      • Approach to Soft Tissue Tumors
      • Bone Pathology
    • Liver Pathology
      • Approach to Liver Biopsies
      • Hepatitis C
    • Pancreas
    • Gallbladder
    • Lung
    • Medical Kidney
    • Unnecessary Thyroid FNAC
    • Salivary Gland
    • Head and Neck
    • Thymus
    • Breast Pathology
    • Transplantation Pathology
    • Immune System
    • Adrenal
    • Uropathology
      • Prostate Pathology
    • Bone
    • Soft Tissue
    • Gynecological Pathology
      • Approach to Endometrial Biopsies
      • Immunohistochemistry in Gynecological Pathology
    • Dermatopathology
    • Organ Independent Pathology
  • Pathology Residents & Pathologists
    • Pathologist
    • So Called Junk Materials & Pitfalls
    • It happens / I have seen that before / Olur öyle
    • Helpful Web Sites for Diagnostic Practice
    • Virtual Slides
    • General Resources For Residents
    • History of Pathology
    • Pathology Reports
    • Mitosis
    • The Future of Pathology
    • Resident Education
    • Rotations of Pathology Residents
    • Web sites of Pathologists
    • Unknowns
    • Photography
    • Pathology Associations
    • Pathology Webinars
    • Pathology as a Career
    • Diagnosis, accuracy, interobserver and intraobserver reliability
    • Pathology News
    • Academic Accounts
    • Academic Tools
    • Moleküler Patoloji'ye Dair
    • jargon
  • Pathology and Social Media
    • Pathology and Social Media
  • Pathology Tweets
    • Pathology Tweets
      • Pathology Tweets
  • Taxonomy and Classification of Diseases
    • Taxonomy and Classification of Diseases
    • Tumor Classification
    • Classification Theory
    • Chaos Theory and Uncertainity
  • Pathophysiology
    • Pathophysiology
  • Carcinogenesis, Hallmarks of Cancer
    • Carcinogenesis & Hallmarks of Cancer
      • Carcinogenesis
      • HPV
      • Tumor Immunology
      • Metastasis
  • Computational, Digital & Mathematical Pathology
    • Digital Pathology
    • Dijital Patoloji'ye Dair
    • About the Usage of Digital Pathology
    • Digital Pathology Software
    • Analysis
    • Telepathology
    • Cytomine
    • Openmicroscopy
    • Articles on computational, digital, and mathematical pathology
    • Mathematical Pathology
    • Image Analysis
  • Macroscopy
    • Macroscopy
    • Whipple Macroscopy
    • Macroscopic Photography
    • Macrocopy Videos
    • Macroscopy Articles & Guidelines
  • Autopsy
    • Autopsy
    • Autopsy Articles
  • Guidelines
    • Guidelines
    • AJCC, UICC, TNM
    • CAP
    • AAPA
  • Treatment and Pathology
    • Treatment
    • Therapy related changes
    • Immunotherapy
    • Prognostic, Predictive and Therapeutic Factors
  • Laboratory Management
    • Laboratory Management
    • Lean
    • Laboratory Information Systems
      • Patoloji Modülü Özellikleri
    • Routine Histology Laboratory
    • Liquid Based Cytology Preperations
    • Research Lab
    • Errors in Pathology
    • Microscopy
    • Health Risks
    • Critical Diagnoses
    • Staff
    • Quality And Standardisation
    • Resume
    • Acreditation
  • Stains
    • Stains
    • Hematoxylin and Eosin
    • Histochemistry
    • Immunohistochemistry
    • Immunohistochemistry Quantification
    • The use of immunohistochemistry for diagnosis
  • Databases and Pathology
    • Databases and Pathology
    • SEER
    • TCGA
    • Filemaker
    • Access
    • PubMed
    • MeSH
    • GLOBOCAN
    • National Cancer Database
  • Pathology and Other Departments
    • Pathology and Other Departments
    • Rotations of Residents to Pathology from Other Departments
    • Surgery and Pathology
    • Radiology and Pathology
    • Genetics and Pathology
    • Oncology and Pathology
    • Endoscopy and Pathology
    • Inadequate specimen? OR pathologist? OR laboratory?
    • Turnaround Time
    • Research Collaboration
    • Epidemiology and Pathology
    • Comperative Pathology
  • Patients and Pathology
    • Patients and Pathology
    • Informing Patients About Pathology
  • Statistics, Bioinformatics, and Pathology
    • Statistics, Bioinformatics, and Pathology
    • Histopatoloji çalışmalarında istatistik için nasıl veri hazırlanır?
    • Statistical Terms
    • Patologlarla istatistikçilerin potansiyel ortak çalışma alanları
  • Statistics and Bioinformatics
    • Statistics and Bioinformatics
    • Orange
    • R-project
      • Online R Books
      • R Education Videos
      • R-project veri yüklemek neden zor?
      • R packages
      • Using multiple R versions
    • SPSS
    • PSPP
    • Text Mining
      • Text Mining Videos
      • Text Mining Related Web Sites
      • Text Mining Journal Articles
      • Text Mining Courses
      • Text Mining Turkish
      • Text Mining Blog Posts Examples
      • Text Mining R
      • Text Mining Orange
      • Text Mining PubMed
      • Text Mining Twitter
      • Text Mining PubMed
    • Bioinformatics
    • Bioconductor
    • Tools for Data Analysis and Visualisation
    • googleVis
    • Data Visualization and R
    • P Value
    • MedCalc
    • Power Analysis
    • ROC analysis
    • Survival Analysis
    • Kaplan Meier
    • JASP
    • Jamovi
    • SAS
    • Statistics and Bioinformatics Education
    • Neural Network
    • Sensitivity, Specificity, Predictive Values & Decision Making
    • Alluvial Diagrams
    • Machine Learning
      • Linear Regression
      • Decision Tree
      • Random Forest
      • Logistic Regression
      • K - Nearest Neighbors
      • Support Vector Machine
      • Naïve Bayes Classifier
      • Cluster Analysis
      • Principal Component Analysis
      • Artificial Neural Networks
      • Apriori Algorithm
      • Association Rules
      • Linear Discriminant Analysis
      • Convolutional Neural Networks
      • Recurrent Neural Networks
    • Statistics General
    • Mathematic Tools
    • Kappa
    • Regression
    • Missing Values
    • Health Data
    • Python
    • Reproducible Reports
  • Writing Journal Articles
    • Writing Journal Articles
    • Finding Relevant Articles
    • Selecting A Journal
    • Rephrasing & Synonyms
    • Figures and Images
    • Plagiarism
    • Writing Journal Articles
    • IRB
    • Text Editing
    • Review
    • Reproducibility
    • Open Access
    • Platform / Oral Presentation
    • Authorship
    • Publishing General
    • Bibliography
      • EndNote
    • Research Planning
    • Citavi
    • Research Quality
    • Citation
    • Visual Abstracts
  • Bibliometrics
    • Bibliometrics
    • Bibliography, Impact Factor, and Citations
    • Research Articles
    • Data And Tools For Bibliographic Analysis
      • Data and Tools
      • VOSviewer
      • CitNetExplorer
      • Sci2Tool
      • CiteSpace
      • Reference Parsing
      • R for PubMed
    • Problems in Bibliometric Analysis
    • Freecite
  • Pathology Meetings
    • Pathology Meetings
    • Organization Of Meetings
  • Science
    • Science
    • Genetics
    • Physics
    • Mathematics & Geometry
    • Neuroscience
    • Academics
    • Cancer Research
    • Medicine
  • Computers
    • Computers
    • Computer Tips
    • Syntax Highlighting
    • Excel, Sheets
    • GitBook Plugins
    • Git GitHub
    • Lecture Preperation
    • Links
  • Games
    • Games
    • Eyewire
    • Go
    • Chess
      • Satranç
      • Videos
  • Appendix
    • Courses and MOOCs
    • Computer Programs and Applications
    • Books
    • Web Pages
    • Videos
    • GitHub Repositories
    • Yazmayıp da beslese miydik
    • Deutsche Artikel
    • Clippings
    • miscellaneous
  • Pathology and Social Media
    • Pathology and Social Media
  • Pathology Tweets
    • Pathology Tweets
      • Pathology Tweets
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  • Git GitHub
  • GitBook Plugins
  • clone a branch
  • Keeping a fork up to date

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  1. Computers

Git GitHub

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Git GitHub

  • Publish blog posts from R + knitr to WordPress

  • A minimal example of building and deploying a blogdown-based website via Travis CI

  • add this to book.json

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  • Gitbook plugin component

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  • YouTube

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  • add this to book.json

{
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    }
  • Gitbook plugin component

{
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  • YouTube

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GitBook Plugins

  • add this to book.json

{
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  • Gitbook plugin component

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  • YouTube

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  • Create a new repository on GitHub. You can also add a gitignore file, a readme and a > licence if you want

  • Open Git Bash

  • Change the current working directory to your local project.

  • Initialize the local directory as a Git repository.

git init
  • Add the files in your new local repository. This stages them for the first commit.

git add .
  • Commit the files that you’ve staged in your local repository.

git commit -m "initial commit"
  • Copy the https url of your newly created repo

  • In the Command prompt, add the URL for the remote repository where your local repository > will be pushed.

git remote add origin 'remote_repository_URL'
git remote -v
  • Push the changes in your local repository to GitHub.

git push -f origin master

clone a branch

git clone --single-branch --branch current-dev https://github.com/jamovi/jamovi.git

Keeping a fork up to date

  1. Clone your fork:

git clone git@github.com:YOUR-USERNAME/YOUR-FORKED-REPO.git
  1. Add remote from original repository in your forked repository:

cd into/cloned/fork-repo
git remote add upstream git://github.com/ORIGINAL-DEV-USERNAME/REPO-YOU-FORKED-FROM.git
git fetch upstream
  1. Updating your fork from original repo to keep up with their changes:

git pull upstream master

Deleting the .git folder may cause problems in your git repository. If you want to delete all your commit history but keep the code in its current state, it is very safe to do it as in the following:

  1. Checkout

    git checkout --orphan latest_branch

  2. Add all the files

    git add -A

  3. Commit the changes

    git commit -am "commit message"

  4. Delete the branch

    git branch -D main

  5. Rename the current branch to main

    git branch -m main

  6. Finally, force update your repository

    git push -f origin main

git - the simple guide
https://yihui.name/knitr/demo/wordpress/
https://travis-blogdown.yihui.name
https://github.com/yihui/travis-blogdown
https://plugins.gitbook.com/plugin/component
https://plugins.gitbook.com/plugin/component
https://plugins.gitbook.com/plugin/component
Adding an existing project to GitHub using the command line
https://www.softwarelab.it/2018/10/12/adding-an-existing-project-to-github-using-the-command-line/
https://github.com/jamovi/jamovi/tree/current-dev
https://gist.github.com/sbalci/9959350f59eda7ca24bd77fe2d21323f
git - how to delete all commit history in github? - Stack Overflow
how to delete all commit history in github?Stack Overflow
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