Merge branch 'master' of github.com:griffithlab/rnabio.org

Gemfile.lock

@@ -41,6 +41,7 @@ GEM
     fiber-local (1.0.0)
     forwardable-extended (2.6.0)
     gemoji (4.1.0)
+    google-protobuf (3.22.3-aarch64-linux)
     google-protobuf (3.22.3-x86_64-darwin)
     hashery (2.1.2)
     html-pipeline (2.14.3)
@@ -105,6 +106,8 @@ GEM
       rb-inotify (~> 0.9, >= 0.9.10)
     mercenary (0.4.0)
     minitest (5.18.0)
+    nokogiri (1.14.3-aarch64-linux)
+      racc (~> 1.4)
     nokogiri (1.14.3-x86_64-darwin)
       racc (~> 1.4)
     pathutil (0.16.2)
@@ -126,6 +129,9 @@ GEM
     rouge (4.1.0)
     ruby-rc4 (0.1.5)
     safe_yaml (1.0.5)
+    sass-embedded (1.62.0)
+      google-protobuf (~> 3.21)
+      rake (>= 10.0.0)
     sass-embedded (1.62.0-x86_64-darwin)
       google-protobuf (~> 3.21)
     terminal-table (3.0.2)
@@ -142,6 +148,7 @@ GEM
     zeitwerk (2.6.7)
 
 PLATFORMS
+  aarch64-linux
   x86_64-darwin-21
 
 DEPENDENCIES

_posts/0009-04-01-Lectures.md

@@ -26,7 +26,40 @@ Organized by [Cold Spring Harbor Laboratory (CSHL)](http://www.cshl.edu/) - [Cou
 
 **Presentations:**
 
-TBA
+* [Emerging next-generation sequencing platforms (Elaine Mardis)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/CSHL_Emerging NGS Platforms_Mardis.pdf)
+* [Overview of Next Generation Short Read Sequencing Technologies (Elaine Mardis)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/CSHL_ShortRead_Mardis.pdf)
+* [Ben Sunkel] 
+* [John McPherson]
+* [Research Applications of Single Cell Sequencing (Trevor Pugh)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/)
+* [Single cell sequencing technology and applications (Jonathan Preall)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/SeqTech_2023_Preall.pdf)
+* [Genomics at scale with the NHGRI AnVIL (Mike Schatz)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/2023.11.07.CSHLSequencing.AnVIL_Schatz.pdf)
+* [Long read sequencing technology and research applications (Richard McCombie)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/)
+* [Zach Lippman]
+* [Interpreting cis-regulatory mechanisms learned by genomic deep learning (Peter Koo)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/2023_Advanced Sequencing Technologies & Bioinformatics Analysis Course_Koo.pdf)
+* [More advanced command line lab and exercise (Jason Kunisaki)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/11_8_2023 - Command Line Lab_Kunisaki.pdf)
+* [Adam Phillippy]
+* [An Overview of Bioinformatics (Chris Miller)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/intro_bioinformatics_Miller.pdf)
+* [Sanja Vickovic]
+* [Concepts in genome coordinates, intervals, and arithmetic (Jason Kunisaki)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/Bedtools Part 1_Kunaski.pdf)
+* [Using bedtools (and awk) to perform genome arithmetic (Jason Kunisaki)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/Bedtools part 2_Kunasaki.pdf)
+* [Noncoding RNAs (Chris Maher)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/)
+* [File formats (Felicia Gomez)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/RNASeq_MiniLecture_02_03_SAM_BAM_BED-2_Gomez.pdf)
+* [Alignment concepts (Felicia Gomez)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/alignment_lecture_3_update_2023_Gomez.pdf)
+* [Jessica Mozersky]
+* [DNA Alignment LAB_CSHL_2023 (Mariam Khanfar)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/DNA Alignment LAB_CSHL_2023_Kahnfar.pdf)
+* [Introduction to IGV (Kartik Singhal)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/RNASeq_Module2_IGV_Tutorial_Brief_Singhal.pdf)
+* [Intro to concepts in variant calling (Chris Miller)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/variant_calling_Miller.pdf)
+* [Mariam Khanfar]
+* [Somatic variant calling (Chris Miller)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/variant_calling_Miller.pdf)
+* [Variant Representation and Interpretation (Wes Goar)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/Variant Interpretation or  Classification CSHL 2023_Goar.pdf)
+* [Introduction to epigenomics - ATAC, ChIPseq and Bisulfite approaches (Chris Miller)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/chipseq_bisulfite_Miller.pdf)
+* [Data Visualization(Chris Miller)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/)
+* [Data Cleaning (Chris Miller)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/)
+* [Single cell ATAC-seq (Yang Li)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/)
+* [Single cell ATAC-seq Part 2 (Yang Li)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/)
+* [Introduction to scRNA analysis (Jonathan Preall)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/)
+* [Epilepsy-affected brain tissues, somatic mosaicism, model organisms (Tracy Bedrosian)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2023/full/)
+
 
 
 ### CBW RNA-seq analysis (July 17-19th, 2023. Toronto, ON, Canada))