-
-
Notifications
You must be signed in to change notification settings - Fork 0
/
README.Rmd
291 lines (177 loc) · 12.8 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r global options, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "100%"
)
```
# Histopathology Research Template 🔬
🔬👀📑🗃📊🏨🗄📇📖⚗📝🎶📈📉📃🖍
🔬🔬🏋🚴🚙👨💻
📸📺🎛🔭🔬💊🔐🍫🌸
---
https://sbalci.github.io/histopathology-template/
---
<a href="https://www.buymeacoffee.com/bS0teIs" target="_blank"><img src="https://cdn.buymeacoffee.com/buttons/arial-orange.png" alt="Buy Me A Coffee" style="height: 51px !important;width: 217px !important;" ></a>
---
<!-- badges: start -->
[](https://gitpod.io/#https://github.com/sbalci/histopathology-template)
<!-- [](https://CRAN.R-project.org/package=histopathology-template) -->
[](https://doi.org/10.5281/zenodo.3635430)
https://doi.org/10.5281/zenodo.3635430
https://osf.io/3tjfk/
[](https://www.repostatus.org/#wip)
[](https://www.tidyverse.org/lifecycle/)
<!-- [](https://travis-ci.com/sbalci/histopathology-template) -->
<!-- [](https://codecov.io/gh/sbalci/histopathology-template) -->
<!-- [](https://ci.appveyor.com/project/sbalci/histopathology-template) -->
<!-- [](https://coveralls.io/github/sbalci/histopathology-template?branch=master) -->
<!-- [](https://circleci.com/gh/sbalci/histopathology-template) -->
<!-- [](https://requires.io/github/sbalci/histopathology-template/requirements/?branch=master) -->
<!-- [](https://libraries.io/github/sbalci/histopathology-template) -->
<!-- [](https://www.codefactor.io/repository/github/sbalci/histopathology-template) -->
<!-- [](https://depshield.github.io) -->
<!-- [](https://dashboard.guardrails.io/default/gh/sbalci/histopathology-template) -->
<!-- [](https://github.com/sbalci/histopathology-template/commits/master) -->
<!-- [](https://CRAN.R-project.org/package=histopathology-template) -->
<!-- [](https://github.com/sbalci/histopathology-template/) -->
<!-- [](https://github.com/sbalci/histopathology-template/issues) -->
<!-- [](https://github.com/sbalci/histopathology-template) -->
<!-- [](https://github.com/sbalci/histopathology-template/network) -->
<!-- [](https://github.com/sbalci/histopathology-template/stargazers) -->
<!-- [](https://sbalci.github.io/histopathology-template/) -->
<!-- [](http://hits.dwyl.io/sbalci/histopathology-template) -->
<!-- [](https://twitter.com/intent/tweet?text=%23rstats%20codes%20for%20histopathology%20research%20by%20@serdarbalci&url=https%3A%2F%2Fgithub.com%2Fsbalci%2Fhistopathology-template) -->
<!--  -->
<!-- [](https://github.com/sbalci/histopathology-template/issues) -->
[](https://sourceforge.net/projects/histopathr/files/latest/download)
[](https://sourceforge.net/projects/histopathr/files/latest/download)
[](https://sourceforge.net/p/histopathr/)
[](https://saythanks.io/to/sbalci)
[](https://mybinder.org/v2/gh/sbalci/histopathology-template/master?urlpath=rstudio)
<!-- badges: end -->
https://github.com/sbalci/histopathology-template
This repository is a template for the codes I use in [my and my friends' histopathology research](https://sbalci.github.io/cv/SerdarBalciMDPathologist.html).
---
**See examples**
- See some of the codes here: https://sbalci.github.io/histopathology-template/Report.html
- You may also install [histopathR](https://sbalci.github.io/histopathR/) package to get all the codes as R Markdown Template.
``` r
devtools::install_github("sbalci/histopathR")
rmarkdown::draft(file = "myfile",
template = "clinicopathological",
package = "histopathR",
create_dir = TRUE,
edit = TRUE)
```
- I have tried to collect common codes in [My R Codes For Data Analysis](https://sbalci.github.io/MyRCodesForDataAnalysis/). I plan to collect them under the package [histopathR](https://sbalci.github.io/histopathR/) gradually.
---
**How to use**
- *In RStudio:*
- Fork this repository. Then use this repository as template as described [here](https://help.github.com/en/articles/creating-a-repository-from-a-template).
- Use RStudio project as described [here](https://happygitwithr.com/existing-github-first.html#new-rstudio-project-via-git-clone-1).
- Do not forget to change chunk functions to `eval = TRUE`.
- This template contains packages using [renv](https://rstudio.github.io/renv/articles/renv.html).
- *Via Docker:*
https://hub.docker.com/r/serdarbalci/clinicopathological
```bash
docker pull serdarbalci/clinicopathological
```
https://twitter.com/serdarbalci/status/1197849208302252032
- *As a standalone app (for mac only):*
https://sourceforge.net/projects/histopathr/
https://twitter.com/serdarbalci/status/1198348640294711296
https://serdarbalci.gitbook.io/parapathology/computers/computers#deploying-a-shiny-app-as-a-desktop-application-with-electron
- *As a Shiny app:*
Launch here:
https://serdarbalci.shinyapps.io/histopathR/
Run in your own computer R session:
```r
library(shiny)
runUrl("https://github.com/sbalci/histopathRshiny/raw/master/histopathRshiny.tar.gz")
```
Code here:
https://github.com/sbalci/histopathRshiny
- *As a jamovi module:*
Download module here:
https://github.com/sbalci/ClinicoPathJamoviModule/raw/master/ClinicoPath.jmo
https://github.com/sbalci/ClinicoPathJamoviModule
https://sourceforge.net/projects/clinicopathjamovimodule/
---
**Recommended Links for Reproducible Research**
- [Reproducible Templates for Analysis and Dissemination](https://www.coursera.org/learn/reproducible-templates-analysis/home/info)
- [Happy Git and GitHub for the useR](https://happygitwithr.com/)
- [R-Giris Dersi Sunum](https://sbalci.github.io/MyRCodesForDataAnalysis/R-Giris.html)
- [R-Giris Dersi](https://sbalci.github.io/MyRCodesForDataAnalysis/R-Giris.nb.html)
- [R-Markdown Dersi Sunum](https://sbalci.github.io/MyRCodesForDataAnalysis/R-Markdown.nb.html)
- [R-Markdown Dersi](https://sbalci.github.io/MyRCodesForDataAnalysis/R-Markdown.html)
- [How to Prepare Data for Histopathology Research pdf](https://sbalci.github.io/MyRCodesForDataAnalysis/How-to-Prepare-Data-for-Histopathology-Research.pdf)
- [How to Prepare Data for Histopathology Research](https://sbalci.github.io/MyRCodesForDataAnalysis/How-to-Prepare-Data-for-Histopathology-Research.nb.html)
- [How to Prepare Data for Histopathology Research Presentation](https://sbalci.github.io/MyRCodesForDataAnalysis/How-to-Prepare-Data-for-Histopathology-Research.html)
- ["The Quartz guide to bad data"nın Türkçe çevirisi: Kötü Veri Kılavuzu ](https://sbalci.github.io/Kotu-Veri-Kilavuzu/)
- [Create A MS Word Template for R Markdown](https://vimeo.com/110804387)
**Please Give Me FeedBack**
https://goo.gl/forms/YjGZ5DHgtPlR1RnB3
---
🔬🔬🔬🔬🔬
UNDER CONSTRUCTION 🛠⛔️⚠️🔩
<!-- https://sbalci.github.io/histopathology-template/ -->
<a class="twitter-follow-button" data-show-count="false" href="https://twitter.com/serdarbalci">Follow @serdarbalci</a><script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
<!-- [](https://github.com/sbalci/histopathology-template/issues) -->
[](https://saythanks.io/to/sbalci)
<!-- [](http://hits.dwyl.io/sbalci/histopathology-template) -->
<!-- --- -->
<!-- 🔬 **I plan to collect codes for future research. I will add some small functions.** -->
<!-- - Methods to import and prepare data for analysis. -->
<!-- - Descriptive statistics. -->
<!-- - Hypothesis tests. -->
<!-- - Survival analysis. -->
<!-- - Regression analysis. -->
<!-- - Cluster analysis. -->
<!-- 🔬 **I plan to make template files to form when loading the package.** -->
<!-- 🔬 **I plan two tutorial files as vignettes:** -->
<!-- - How to prepare data for histopathological research -->
<!-- - How to analyse data for histopathological research -->
---
{% if page.comments %}
<script id="dsq-count-scr" src="//https-sbalci-github-io.disqus.com/count.js" async></script>
<div id="disqus_thread"></div>
<script>
/**
* RECOMMENDED CONFIGURATION VARIABLES: EDIT AND UNCOMMENT THE SECTION BELOW TO INSERT DYNAMIC VALUES FROM YOUR PLATFORM OR CMS.
* LEARN WHY DEFINING THESE VARIABLES IS IMPORTANT: https://disqus.com/admin/universalcode/#configuration-variables*/
/*
var disqus_config = function () {
this.page.url = PAGE_URL; // Replace PAGE_URL with your page's canonical URL variable
this.page.identifier = PAGE_IDENTIFIER; // Replace PAGE_IDENTIFIER with your page's unique identifier variable
};
*/
(function() { // DON'T EDIT BELOW THIS LINE
var d = document, s = d.createElement('script');
s.src = 'https://https-sbalci-github-io.disqus.com/embed.js';
s.setAttribute('data-timestamp', +new Date());
(d.head || d.body).appendChild(s);
})();
</script>
<noscript>Please enable JavaScript to view the <a href="https://disqus.com/?ref_noscript">comments powered by Disqus.</a></noscript>
{% endif %}
---
<hr />
<p style="text-align: center;">A work by <a href="https://github.com/sbalci/">Serdar Balci</a></p>
<p style="text-align: center;"><span style="color: #808080;"><em>[email protected]</em></span></p>
<!-- Add icon library -->
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/4.7.0/css/font-awesome.min.css">
<!-- Add font awesome icons -->
<p style="text-align: center;">
<a href="https://twitter.com/serdarbalci" class="fa fa-twitter"></a>
<a href="https://www.linkedin.com/in/serdar-balci-md-pathologist/" class="fa fa-linkedin"></a>
<a href="https://github.com/sbalci/" class="fa fa-github"></a>
</p>