merge conflict

socalrug · Aug 26, 2019 · 7d76140 · 7d76140
2 parents f15146c + 34ff5bb
commit 7d76140
Show file tree

Hide file tree

Showing 49 changed files with 2,195 additions and 1 deletion.
diff --git a/..._extracting_topics_from_cancer_patients_mutational_profiles/Extracting topics 📚 from.html b/..._extracting_topics_from_cancer_patients_mutational_profiles/Extracting topics 📚 from.html
diff --git a/...rom_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/1536.png b/...rom_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/1536.png
diff --git a/...mutational_profiles/Extracting topics 📚 from_files/1_RV087VG2ntly7mIEEML2oQ.gif b/...mutational_profiles/Extracting topics 📚 from_files/1_RV087VG2ntly7mIEEML2oQ.gif
diff --git a/...mutational_profiles/Extracting topics 📚 from_files/1_YN48zFbH6sEpOe-cbBjfbg.gif b/...mutational_profiles/Extracting topics 📚 from_files/1_YN48zFbH6sEpOe-cbBjfbg.gif
diff --git a/...om_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/MathJax.js.download b/...om_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/MathJax.js.download
diff --git a/...ients_mutational_profiles/Extracting topics 📚 from_files/Signature_patterns.png b/...ients_mutational_profiles/Extracting topics 📚 from_files/Signature_patterns.png
diff --git a/...cancer_patients_mutational_profiles/Extracting topics 📚 from_files/analysis.png b/...cancer_patients_mutational_profiles/Extracting topics 📚 from_files/analysis.png
diff --git a/...rom_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/book.jpg b/...rom_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/book.jpg
diff --git a/...om_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/book2.png b/...om_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/book2.png
diff --git a/..._cancer_patients_mutational_profiles/Extracting topics 📚 from_files/compare.png b/..._cancer_patients_mutational_profiles/Extracting topics 📚 from_files/compare.png
diff --git a/...cer_patients_mutational_profiles/Extracting topics 📚 from_files/dataprocess.png b/...cer_patients_mutational_profiles/Extracting topics 📚 from_files/dataprocess.png
diff --git a/...rom_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/dogs.png b/...rom_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/dogs.png
diff --git a/...ancer_patients_mutational_profiles/Extracting topics 📚 from_files/fontawesome-all.min.css b/...ancer_patients_mutational_profiles/Extracting topics 📚 from_files/fontawesome-all.min.css
diff --git a/..._cancer_patients_mutational_profiles/Extracting topics 📚 from_files/history.png b/..._cancer_patients_mutational_profiles/Extracting topics 📚 from_files/history.png
diff --git a/...ancer_patients_mutational_profiles/Extracting topics 📚 from_files/mcmcplots.png b/...ancer_patients_mutational_profiles/Extracting topics 📚 from_files/mcmcplots.png
diff --git a/...ncer_patients_mutational_profiles/Extracting topics 📚 from_files/membership.PNG b/...ncer_patients_mutational_profiles/Extracting topics 📚 from_files/membership.PNG
diff --git a/...rom_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/meme.png b/...rom_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/meme.png
diff --git a/...om_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/meme2.png b/...om_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/meme2.png
diff --git a/..._from_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/mp.jpg b/..._from_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/mp.jpg
diff --git a/...ancer_patients_mutational_profiles/Extracting topics 📚 from_files/mutations.png b/...ancer_patients_mutational_profiles/Extracting topics 📚 from_files/mutations.png
diff --git a/...pics_from_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/my-style.css b/...pics_from_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/my-style.css
@@ -0,0 +1,62 @@
+@import url(https://fonts.googleapis.com/css?family=Roboto+Slab:400);
+@import url(https://fonts.googleapis.com/css?family=Inconsolata);
+
+.image-50 img {
+  width: 50%;
+}
+
+.image-200 img {
+  width: 200%;
+}
+
+
+.red { color: #910c07; }
+
+.bl { color: #525252; }
+
+.blue { color: #33b2db; }
+
+.small { font-size: 25px;}
+
+.median { font-size: 35px;}
+
+.grey {color:#dbdde4;}
+
+body {
+  font-family: 'Roboto Slab', serif;
+  font-weight: normal;
+  color: #272822;
+}
+h1, h2, h3, h4 {
+  font-family: 'Roboto Slab', serif;
+  font-weight: normal;
+}
+.remark-code, .remark-inline-code {
+  font-family: 'Inconsolata', monospace;
+}
+
+.remark-slide-content h1 {
+    font-size: 50px;
+}
+
+.remark-slide-content h2 {
+    font-size: 40px;
+}
+
+.remark-slide-content h3 {
+    font-size: 35px;
+    color: #525252;
+}
+
+.remark-slide-content h4 {
+    font-size: 25px;
+}
+
+.footnote {
+  color: #910c07;
+  position: absolute;
+  bottom: 1em;
+  padding-right: 4em;
+  font-size: 0.6em;
+}
+
diff --git a/...om_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/panel.png b/...om_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/panel.png
diff --git a/...rom_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/pole.png b/...rom_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/pole.png
diff --git a/...om_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/pole2.png b/...om_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/pole2.png
diff --git a/...patients_mutational_profiles/Extracting topics 📚 from_files/remark-latest.min.js.download b/...patients_mutational_profiles/Extracting topics 📚 from_files/remark-latest.min.js.download
diff --git a/...patients_mutational_profiles/Extracting topics 📚 from_files/sagemaker-ntm-6.gif b/...patients_mutational_profiles/Extracting topics 📚 from_files/sagemaker-ntm-6.gif
diff --git a/...ncer_patients_mutational_profiles/Extracting topics 📚 from_files/screenshot.png b/...ncer_patients_mutational_profiles/Extracting topics 📚 from_files/screenshot.png
diff --git a/...om_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/shiny.png b/...om_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/shiny.png
diff --git a/...rom_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/sigs.png b/...rom_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/sigs.png
diff --git a/...m_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/single.png b/...m_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/single.png
diff --git a/..._cancer_patients_mutational_profiles/Extracting topics 📚 from_files/smoking.png b/..._cancer_patients_mutational_profiles/Extracting topics 📚 from_files/smoking.png
diff --git a/...cancer_patients_mutational_profiles/Extracting topics 📚 from_files/smoking2.png b/...cancer_patients_mutational_profiles/Extracting topics 📚 from_files/smoking2.png
diff --git a/...cancer_patients_mutational_profiles/Extracting topics 📚 from_files/spectrum.png b/...cancer_patients_mutational_profiles/Extracting topics 📚 from_files/spectrum.png
diff --git a/...rom_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/stan.png b/...rom_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/stan.png
diff --git a/...from_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/str.png b/...from_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/str.png
diff --git a/...ancer_patients_mutational_profiles/Extracting topics 📚 from_files/subgroups.jpg b/...ancer_patients_mutational_profiles/Extracting topics 📚 from_files/subgroups.jpg
diff --git a/...cancer_patients_mutational_profiles/Extracting topics 📚 from_files/sunlight.png b/...cancer_patients_mutational_profiles/Extracting topics 📚 from_files/sunlight.png
diff --git a/...ancer_patients_mutational_profiles/Extracting topics 📚 from_files/sunlight2.png b/...ancer_patients_mutational_profiles/Extracting topics 📚 from_files/sunlight2.png
diff --git a/...rom_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/tcga.png b/...rom_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/tcga.png
diff --git a/...m_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/topics.png b/...m_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/topics.png
diff --git a/...ancer_patients_mutational_profiles/Extracting topics 📚 from_files/twogroups.png b/...ancer_patients_mutational_profiles/Extracting topics 📚 from_files/twogroups.png
diff --git a/...ients_mutational_profiles/Extracting topics 📚 from_files/unnamed-chunk-12-1.png b/...ients_mutational_profiles/Extracting topics 📚 from_files/unnamed-chunk-12-1.png
diff --git a/...ients_mutational_profiles/Extracting topics 📚 from_files/unnamed-chunk-13-1.png b/...ients_mutational_profiles/Extracting topics 📚 from_files/unnamed-chunk-13-1.png
diff --git a/...tients_mutational_profiles/Extracting topics 📚 from_files/unnamed-chunk-7-1.png b/...tients_mutational_profiles/Extracting topics 📚 from_files/unnamed-chunk-7-1.png
diff --git a/...om_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/words.png b/...om_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/words.png
diff --git a/...om_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/xaringan-themer.css b/...om_cancer_patients_mutational_profiles/Extracting topics 📚 from_files/xaringan-themer.css
@@ -0,0 +1,175 @@
+/* -------------------------------------------------------
+ *
+ *     !! This file was generated by xaringanthemer !!
+ *
+ *  Changes made to this file directly will be overwritten
+ *  if you used xaringanthemer in your xaringan slides Rmd
+ *
+ *  Issues or likes?
+ *    - https://github.com/gadenbuie/xaringanthemer
+ *    - https://www.garrickadenbuie.com
+ *
+ *  Need help? Try:
+ *    - vignette(package = "xaringanthemer")
+ *    - ?xaringanthemer::write_xaringan_theme
+ *    - xaringan wiki: https://github.com/yihui/xaringan/wiki
+ *    - remarkjs wiki: https://github.com/gnab/remark/wiki
+ *
+ * ------------------------------------------------------- */
+@import url(https://fonts.googleapis.com/css?family=Droid+Serif:400,700,400italic);
+@import url(https://fonts.googleapis.com/css?family=Yanone+Kaffeesatz);
+@import url(https://cdn.rawgit.com/tonsky/FiraCode/1.204/distr/fira_code.css);
+
+
+body {
+  font-family: 'Droid Serif', 'Palatino Linotype', 'Book Antiqua', Palatino, 'Microsoft YaHei', 'Songti SC', serif;
+  font-weight: normal;
+  color: #272822;
+}
+h1, h2, h3 {
+  font-family: 'Yanone Kaffeesatz';
+  font-weight: normal;
+  color: #2d8183;
+}
+.remark-slide-content {
+  background-color: #FFFFFF;
+  font-size: 20px;
+
+
+
+  padding: 1em 4em 1em 4em;
+}
+.remark-slide-content h1 {
+    font-size: 55px;
+}
+.remark-slide-content h2 {
+    font-size: 45px;
+}
+.remark-slide-content h3 {
+    font-size: 35px;
+}
+.remark-code, .remark-inline-code {
+  font-family: 'Fira Code', 'Lucida Console', Monaco, monospace;
+}
+.remark-code {
+  font-size: 0.9em;
+}
+.remark-inline-code {
+  font-size: 1em;
+  color: #2d8183;
+
+
+}
+.remark-slide-number {
+  color: #2d8183;
+  opacity: 1;
+  font-size: 0.9em;
+}
+strong{color:#2d8183;}
+a, a > code {
+  color: #2d8183;
+  text-decoration: none;
+}
+.footnote {
+
+  position: absolute;
+  bottom: 3em;
+  padding-right: 4em;
+  font-size: 0.9em;
+}
+.remark-code-line-highlighted {
+  background-color: rgba(255,255,0,0.5);
+}
+.inverse {
+  background-color: #2d8183;
+  color: #FFFFFF;
+
+}
+.inverse h1, .inverse h2, .inverse h3 {
+  color: #FFFFFF;
+}
+.title-slide, .title-slide h1, .title-slide h2, .title-slide h3 {
+  color: #FFFFFF;
+}
+.title-slide {
+  background-color: #2d8183;
+
+
+
+}
+.title-slide .remark-slide-number {
+  display: none;
+}
+/* Two-column layout */
+.left-column {
+  width: 20%;
+  height: 92%;
+  float: left;
+}
+.left-column h2, .left-column h3 {
+  color: #2d818399;
+}
+.left-column h2:last-of-type, .left-column h3:last-child {
+  color: #2d8183;
+}
+.right-column {
+  width: 75%;
+  float: right;
+  padding-top: 1em;
+}
+.pull-left {
+  float: left;
+  width: 47%;
+}
+.pull-right {
+  float: right;
+  width: 47%;
+}
+.pull-right ~ * {
+  clear: both;
+}
+img, video, iframe {
+  max-width: 100%;
+}
+blockquote {
+  border-left: solid 5px #2d818380;
+  padding-left: 1em;
+}
+.remark-slide table {
+  margin: auto;
+  border-top: 1px solid #666;
+  border-bottom: 1px solid #666;
+}
+.remark-slide table thead th { border-bottom: 1px solid #ddd; }
+th, td { padding: 5px; }
+.remark-slide thead, .remark-slide tfoot, .remark-slide tr:nth-child(even) { background: #C0D9D9 }
+table.dataTable tbody {
+  background-color: #FFFFFF;
+  color: #272822;
+}
+table.dataTable.display tbody tr.odd {
+  background-color: #FFFFFF;
+}
+table.dataTable.display tbody tr.even {
+  background-color: #C0D9D9;
+}
+table.dataTable.hover tbody tr:hover, table.dataTable.display tbody tr:hover {
+  background-color: rgba(255, 255, 255, 0.5);
+}
+.dataTables_wrapper .dataTables_length, .dataTables_wrapper .dataTables_filter, .dataTables_wrapper .dataTables_info, .dataTables_wrapper .dataTables_processing, .dataTables_wrapper .dataTables_paginate {
+  color: #272822;
+}
+.dataTables_wrapper .dataTables_paginate .paginate_button {
+  color: #272822 !important;
+}
+
+@page { margin: 0; }
+@media print {
+  .remark-slide-scaler {
+    width: 100% !important;
+    height: 100% !important;
+    transform: scale(1) !important;
+    top: 0 !important;
+    left: 0 !important;
+  }
+}
diff --git a/2019-07-30_extracting_topics_from_cancer_patients_mutational_profiles/Links.txt b/2019-07-30_extracting_topics_from_cancer_patients_mutational_profiles/Links.txt
@@ -0,0 +1,5 @@
+Topic modeling in cancer patients' mutational profiles
+
+https://lda-mutations.netlify.com/#1
+
+https://github.com/zhiiiyang
diff --git a/2019-07-30_extracting_topics_from_cancer_patients_mutational_profiles/README.md b/2019-07-30_extracting_topics_from_cancer_patients_mutational_profiles/README.md
@@ -0,0 +1,16 @@
+# Topic modeling in cancer patients' mutational profiles
+
+* 2019-07-30
+* Speaker: Zhi Yang
+
+## Abstract
+
+Topic models allow us to access the contribution of each topic and its
+representations across different documents. Human genomes have been
+exposed to an assortment of mutational processes by contributing to
+unique patterns of somatic mutations. What would happen if we apply
+the same concept to the somatic mutations obtained from the cancer
+patients and look for “topics” of mutations? I will introduce a simple
+example of Latent Dirichlet Allocation (LDA) and its application in
+investigating cancer patients' mutational profiles in addition to
+available Bayesian tools in R to conduct statistical inference.
diff --git a/README.md b/README.md
@@ -6,8 +6,9 @@ Presentation materials from our monthly meetings
 
 ## 2019 ##
 
+* 08/27/2019: *Olga Korosteleva*, [Regression Models for Count Data](https://github.com/ocrug/presentations/tree/master/2019-08-27_regression_models_for_count_data/)
 
-* 08/27/2019: *John Peach*, [Regression Models for Count Data](https://github.com/ocrug/presentations/tree/master/2019-08-27_regression_models_for_count_data/)
+* 07/30/2019: *Zhi Yang*, [Topic modeling in cancer patients' mutational profiles](https://github.com/ocrug/presentations/tree/master/2019-07-30_extracting_topics_from_cancer_patients_mutational_profiles)
 
 * 07/30/2019: *John Peach*, [Error and Condition Handling in R](https://github.com/ocrug/presentations/tree/master/2019-07-30_error_and_condition_handling_in_R/)