diff --git a/_posts/0009-04-01-Lectures.md b/_posts/0009-04-01-Lectures.md index 516d0f4..553278a 100644 --- a/_posts/0009-04-01-Lectures.md +++ b/_posts/0009-04-01-Lectures.md @@ -30,7 +30,7 @@ Organized by [Cold Spring Harbor Laboratory (CSHL)](http://www.cshl.edu/) - [Cou * [Spatial Transcriptomics (Corinne Strawser)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2024/full/Spatial_Transcriptomics_Corinne_Strawser.pdf) * [Ethics and Regulation of Genomic Research (Jessica Mozersky-virtual lecture)]() * [An Overview of Bioinformatics (Felicia Gomez)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2024/full/An_Overview_of_Bioinformatics_Felicia_Gomez.pptx) -* [Introduction to Unix/Command Line Lab (Felicia Gomez)](https://github.com/griffithlab/rnabio.org/blob/master/posts/0000-08-01-Unix) +* [Introduction to Unix/Command Line Lab (Felicia Gomez)](https://rnabio.org/module-00-setup/0000/08/01/Unix/) * [Intro to cloud computing (My Hoang)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2024/full/RNASeq_Module0_CloudComputing.pdf) * [More advanced command line lab and exercise (Jason Kunisaki)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2024/full/More_advanced_Command_Line_Lab_&_Exercise_Jason_Kunisaki.pptx) * [File formats (Mariam Khanfar)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2024/full/File_Format_Mariam_Khanfar.pdf) @@ -41,23 +41,23 @@ Organized by [Cold Spring Harbor Laboratory (CSHL)](http://www.cshl.edu/) - [Cou * [Bioinformatics in Python (Jason Williams)](https://swcarpentry.github.io/python-novice-gapminder/) * [DNA Alignment LAB (Mariam Khanfar)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2024/full/DNA_Alignment_Lab_Mariam_Khanfar.pdf) * [Massively Parallel Assays (Justin Kinney)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2024/full/Massively_Parallel_Assays_Justin_Kinney.pdf) -* [Introduction to R (Katie Campbell)](https://github.com/griffithlab/rnabio.org/blob/master/posts/0000-08-02-CSHL_Intro_to_R_programming) +* [Introduction to R (Katie Campbell)](https://rnabio.org/module-00-setup/0000/08/02/CSHL_Intro_to_R_programming/) * [Introduction to IGV (Kartik Singhal)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2024/full/IGV_Tutorial_Kartik_Singhal.pdf) * [Introduction to bulk RNA-sequencing (Malachi Griffith)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2024/full/RNASeq_Module1_IntrotoRNA.pdf) -* [Environment and tool installation lab (Obi Griffith)](https://github.com/griffithlab/rnabio.org/blob/master/posts/0000-09-01-Environment) -* [Reference, annotations, indexing, data and QC lab (Obi Griffith)](https://github.com/griffithlab/rnabio.org/blob/master/posts/0001-02-01-Reference_Genomes) -* [Alignment lab (Arpad Danos)](https://github.com/griffithlab/rnabio.org/blob/master/posts/0002-03-01-Alignment) +* [Environment and tool installation lab (Obi Griffith)](https://rnabio.org/module-00-setup/0000/09/01/Environment/) +* [Reference, annotations, indexing, data and QC lab (Obi Griffith)](https://rnabio.org/module-01-inputs/0001/02/01/Reference_Genomes/) +* [Alignment lab (Arpad Danos)](https://rnabio.org/module-02-alignment/0002/03/01/Alignment/) * [Alignment and visualization concepts(Arpad Danos)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2024/mini/RNASeq_MiniLecture_02_01_Alignment.pdf) -* [Alignment visualization lab (Malachi Griffith)](https://github.com/griffithlab/rnabio.org/blob/master/posts/0002-05-01-AlignVis_Prep) -* [Post alignment QC lab (Malachi Griffith)](https://github.com/griffithlab/rnabio.org/blob/master/posts/0002-06-01-Alignment_QC) +* [Alignment visualization lab (Malachi Griffith)](https://rnabio.org/module-02-alignment/0002/05/01/AlignVis_Prep/) +* [Post alignment QC lab (Malachi Griffith)](https://rnabio.org/module-02-alignment/0002/06/01/Alignment_QC/) * [Introduction to Expression and Differential Expression Analysis (Obi Griffith)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2024/full/RNASeq_Module3_AbundanceEstimation_DifferentialExpression.pdf) -* [Expression and Differential Expression analysis (Obi Griffith)](https://github.com/griffithlab/rnabio.org/blob/master/posts/0003-01-01-Intro_to_Expression) -* [Expression analysis lab (Obi Griffith)](https://github.com/griffithlab/rnabio.org/blob/master/posts/0003-02-01-Expression) -* [Differential expression lab (My Hoang)](https://github.com/griffithlab/rnabio.org/blob/master/posts/0003-03-01-Differential_Expression-Ballgown) -* [Differential expression visualization and interpretation lab (Malachi Griffith)](https://github.com/griffithlab/rnabio.org/blob/master/posts/0003-04-01-DE_Visualization_Ballgown) -* [Differential expression pathway analysis lab (Obi Griffith)](https://github.com/griffithlab/rnabio.org/blob/master/posts/0003-05-01-DE_Pathway_Analysis) -* [Batch correction lab (Malachi Griffith)](https://github.com/griffithlab/rnabio.org/blob/master/posts/0003-06-01-Batch-Correction-Prep) -* [Alignment free analysis lab (Malachi Griffith)](https://github.com/griffithlab/rnabio.org/blob/master/posts/0004-02-01-Alignment_Free_Kallisto) +* [Expression and Differential Expression analysis (Obi Griffith)](https://rnabio.org/module-03-expression/0003/01/01/Intro_to_Expression/) +* [Expression analysis lab (Obi Griffith)](https://rnabio.org/module-03-expression/0003/02/01/Expression/) +* [Differential expression lab (My Hoang)](https://rnabio.org/module-03-expression/0003/03/01/Differential_Expression-Ballgown/) +* [Differential expression visualization and interpretation lab (Malachi Griffith)](https://rnabio.org/module-03-expression/0003/04/01/DE_Visualization_Ballgown/) +* [Differential expression pathway analysis lab (Obi Griffith)](https://rnabio.org/module-03-expression/0003/05/01/DE_Pathway_Analysis/) +* [Batch correction lab (Malachi Griffith)](https://rnabio.org/module-03-expression/0003/06/01/Batch-Correction-Prep/) +* [Alignment free analysis lab (Malachi Griffith)](https://rnabio.org/module-04-kallisto/0004/02/01/Alignment_Free_Kallisto/) * [Introduction to epigenomics - ATAC, ChIPseq and Bisulfite approaches (Chris Miller)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2024/full/Introduction_to_Epigenomics_ATAC_ChIPseq_Bisulfite_Chris_Miller.pdf) * [Epigenomics lab - Peak Calling (Kartik Singhal)](https://pmbio.org/module-10-appendix/0010/06/01/ChIP-seq_analysis/) * [Long Read Sequencing (Chris Miller)](https://github.com/griffithlab/rnabio.org/blob/master/assets/lectures/cshl/2024/full/Long_Read_Sequencing_Chris_Miller.pdf)