diff --git a/manuscript/1-Introduction.md b/manuscript/1-Introduction.md new file mode 100644 index 00000000..0b0391d7 --- /dev/null +++ b/manuscript/1-Introduction.md @@ -0,0 +1,7 @@ +# 1 Introduction + +{type: iframe, title:1 Introduction, width:800, height:600, poster:resources/chapt_screen_images/introduction.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/introduction.html) + + + diff --git a/manuscript/10-Whole-Genome-or-Exome-Sequencing.md b/manuscript/10-Whole-Genome-or-Exome-Sequencing.md new file mode 100644 index 00000000..47ee8f21 --- /dev/null +++ b/manuscript/10-Whole-Genome-or-Exome-Sequencing.md @@ -0,0 +1,7 @@ +# 10 Whole Genome or Exome Sequencing + +{type: iframe, title:10 Whole Genome or Exome Sequencing, width:800, height:600, poster:resources/chapt_screen_images/whole-genome-or-exome-sequencing.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/whole-genome-or-exome-sequencing.html) + + + diff --git a/manuscript/11-RNA-Methods-Overview.md b/manuscript/11-RNA-Methods-Overview.md new file mode 100644 index 00000000..29d07ff4 --- /dev/null +++ b/manuscript/11-RNA-Methods-Overview.md @@ -0,0 +1,7 @@ +# 11 RNA Methods Overview + +{type: iframe, title:11 RNA Methods Overview, width:800, height:600, poster:resources/chapt_screen_images/rna-methods-overview.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/rna-methods-overview.html) + + + diff --git a/manuscript/12-Bulk-RNA-seq.md b/manuscript/12-Bulk-RNA-seq.md new file mode 100644 index 00000000..173dce66 --- /dev/null +++ b/manuscript/12-Bulk-RNA-seq.md @@ -0,0 +1,7 @@ +# 12 Bulk RNA-seq + +{type: iframe, title:12 Bulk RNA-seq, width:800, height:600, poster:resources/chapt_screen_images/bulk-rna-seq-1.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/bulk-rna-seq-1.html) + + + diff --git a/manuscript/13-Single-cell-RNA-seq.md b/manuscript/13-Single-cell-RNA-seq.md new file mode 100644 index 00000000..4777e5d6 --- /dev/null +++ b/manuscript/13-Single-cell-RNA-seq.md @@ -0,0 +1,7 @@ +# 13 Single-cell RNA-seq + +{type: iframe, title:13 Single-cell RNA-seq, width:800, height:600, poster:resources/chapt_screen_images/single-cell-rna-seq.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/single-cell-rna-seq.html) + + + diff --git a/manuscript/14-Spatial-transcriptomics.md b/manuscript/14-Spatial-transcriptomics.md new file mode 100644 index 00000000..d55c4f0b --- /dev/null +++ b/manuscript/14-Spatial-transcriptomics.md @@ -0,0 +1,7 @@ +# 14 Spatial transcriptomics + +{type: iframe, title:14 Spatial transcriptomics, width:800, height:600, poster:resources/chapt_screen_images/spatial-transcriptomics-1.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/spatial-transcriptomics-1.html) + + + diff --git a/manuscript/15-Chromatin-Methods-Overview.md b/manuscript/15-Chromatin-Methods-Overview.md new file mode 100644 index 00000000..9da81b99 --- /dev/null +++ b/manuscript/15-Chromatin-Methods-Overview.md @@ -0,0 +1,7 @@ +# 15 Chromatin Methods Overview + +{type: iframe, title:15 Chromatin Methods Overview, width:800, height:600, poster:resources/chapt_screen_images/chromatin-methods-overview.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/chromatin-methods-overview.html) + + + diff --git a/manuscript/16-ATAC-Seq.md b/manuscript/16-ATAC-Seq.md new file mode 100644 index 00000000..62eee119 --- /dev/null +++ b/manuscript/16-ATAC-Seq.md @@ -0,0 +1,7 @@ +# 16 ATAC-Seq + +{type: iframe, title:16 ATAC-Seq, width:800, height:600, poster:resources/chapt_screen_images/atac-seq-1.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/atac-seq-1.html) + + + diff --git a/manuscript/17-Single-cell-ATAC-Seq.md b/manuscript/17-Single-cell-ATAC-Seq.md new file mode 100644 index 00000000..8a9ec51b --- /dev/null +++ b/manuscript/17-Single-cell-ATAC-Seq.md @@ -0,0 +1,7 @@ +# 17 Single cell ATAC-Seq + +{type: iframe, title:17 Single cell ATAC-Seq, width:800, height:600, poster:resources/chapt_screen_images/single-cell-atac-seq-1.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/single-cell-atac-seq-1.html) + + + diff --git a/manuscript/18-ChIP-Seq.md b/manuscript/18-ChIP-Seq.md new file mode 100644 index 00000000..8f8d8ae7 --- /dev/null +++ b/manuscript/18-ChIP-Seq.md @@ -0,0 +1,7 @@ +# 18 ChIP-Seq + +{type: iframe, title:18 ChIP-Seq, width:800, height:600, poster:resources/chapt_screen_images/chip-seq-1.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/chip-seq-1.html) + + + diff --git a/manuscript/19-CUT&RUN-and-CUT&Tag.md b/manuscript/19-CUT&RUN-and-CUT&Tag.md new file mode 100644 index 00000000..2c5c608c --- /dev/null +++ b/manuscript/19-CUT&RUN-and-CUT&Tag.md @@ -0,0 +1,7 @@ +# 19 CUT&RUN and CUT&Tag + +{type: iframe, title:19 CUT&RUN and CUT&Tag, width:800, height:600, poster:resources/chapt_screen_images/cutrun-and-cuttag.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/cutrun-and-cuttag.html) + + + diff --git a/manuscript/2-A-Very-General-Genomics-Overview.md b/manuscript/2-A-Very-General-Genomics-Overview.md new file mode 100644 index 00000000..1e11e2b9 --- /dev/null +++ b/manuscript/2-A-Very-General-Genomics-Overview.md @@ -0,0 +1,7 @@ +# 2 A Very General Genomics Overview + +{type: iframe, title:2 A Very General Genomics Overview, width:800, height:600, poster:resources/chapt_screen_images/a-very-general-genomics-overview.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/a-very-general-genomics-overview.html) + + + diff --git a/manuscript/20-DNA-Methylation-Sequencing.md b/manuscript/20-DNA-Methylation-Sequencing.md new file mode 100644 index 00000000..5fdc317a --- /dev/null +++ b/manuscript/20-DNA-Methylation-Sequencing.md @@ -0,0 +1,7 @@ +# 20 DNA Methylation Sequencing + +{type: iframe, title:20 DNA Methylation Sequencing, width:800, height:600, poster:resources/chapt_screen_images/dna-methylation-sequencing.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/dna-methylation-sequencing.html) + + + diff --git a/manuscript/21-Microbiome-Sequencing.md b/manuscript/21-Microbiome-Sequencing.md new file mode 100644 index 00000000..8b3ebcb5 --- /dev/null +++ b/manuscript/21-Microbiome-Sequencing.md @@ -0,0 +1,7 @@ +# 21 Microbiome Sequencing + +{type: iframe, title:21 Microbiome Sequencing, width:800, height:600, poster:resources/chapt_screen_images/microbiome-sequencing.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/microbiome-sequencing.html) + + + diff --git a/manuscript/22-ITCR--omic-Tool-Glossary.md b/manuscript/22-ITCR--omic-Tool-Glossary.md new file mode 100644 index 00000000..c2fbff3a --- /dev/null +++ b/manuscript/22-ITCR--omic-Tool-Glossary.md @@ -0,0 +1,7 @@ +# 22 ITCR -omic Tool Glossary + +{type: iframe, title:22 ITCR -omic Tool Glossary, width:800, height:600, poster:resources/chapt_screen_images/itcr--omic-tool-glossary.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/itcr--omic-tool-glossary.html) + + + diff --git a/manuscript/3-Guidelines-for-Good-Metadata.md b/manuscript/3-Guidelines-for-Good-Metadata.md new file mode 100644 index 00000000..1db61abb --- /dev/null +++ b/manuscript/3-Guidelines-for-Good-Metadata.md @@ -0,0 +1,7 @@ +# 3 Guidelines for Good Metadata + +{type: iframe, title:3 Guidelines for Good Metadata, width:800, height:600, poster:resources/chapt_screen_images/guidelines-for-good-metadata.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/guidelines-for-good-metadata.html) + + + diff --git a/manuscript/4-Considerations-for-choosing-tools.md b/manuscript/4-Considerations-for-choosing-tools.md new file mode 100644 index 00000000..f5fd8906 --- /dev/null +++ b/manuscript/4-Considerations-for-choosing-tools.md @@ -0,0 +1,7 @@ +# 4 Considerations for choosing tools + +{type: iframe, title:4 Considerations for choosing tools, width:800, height:600, poster:resources/chapt_screen_images/considerations-for-choosing-tools.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/considerations-for-choosing-tools.html) + + + diff --git a/manuscript/5-General-Data-Analysis-Tools.md b/manuscript/5-General-Data-Analysis-Tools.md new file mode 100644 index 00000000..e6c0ca72 --- /dev/null +++ b/manuscript/5-General-Data-Analysis-Tools.md @@ -0,0 +1,7 @@ +# 5 General Data Analysis Tools + +{type: iframe, title:5 General Data Analysis Tools, width:800, height:600, poster:resources/chapt_screen_images/general-data-analysis-tools.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/general-data-analysis-tools.html) + + + diff --git a/manuscript/6-Sequencing-Data.md b/manuscript/6-Sequencing-Data.md new file mode 100644 index 00000000..c5a6d048 --- /dev/null +++ b/manuscript/6-Sequencing-Data.md @@ -0,0 +1,7 @@ +# 6 Sequencing Data + +{type: iframe, title:6 Sequencing Data, width:800, height:600, poster:resources/chapt_screen_images/sequencing-data.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/sequencing-data.html) + + + diff --git a/manuscript/7-Microarray-Data.md b/manuscript/7-Microarray-Data.md new file mode 100644 index 00000000..ef451e3c --- /dev/null +++ b/manuscript/7-Microarray-Data.md @@ -0,0 +1,7 @@ +# 7 Microarray Data + +{type: iframe, title:7 Microarray Data, width:800, height:600, poster:resources/chapt_screen_images/microarray-data.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/microarray-data.html) + + + diff --git a/manuscript/8-Annotating-Genomes.md b/manuscript/8-Annotating-Genomes.md new file mode 100644 index 00000000..0c4a7b2d --- /dev/null +++ b/manuscript/8-Annotating-Genomes.md @@ -0,0 +1,7 @@ +# 8 Annotating Genomes + +{type: iframe, title:8 Annotating Genomes, width:800, height:600, poster:resources/chapt_screen_images/annotating-genomes.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/annotating-genomes.html) + + + diff --git a/manuscript/9-DNA-Methods-Overview.md b/manuscript/9-DNA-Methods-Overview.md new file mode 100644 index 00000000..7739b2fb --- /dev/null +++ b/manuscript/9-DNA-Methods-Overview.md @@ -0,0 +1,7 @@ +# 9 DNA Methods Overview + +{type: iframe, title:9 DNA Methods Overview, width:800, height:600, poster:resources/chapt_screen_images/dna-methods-overview.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/dna-methods-overview.html) + + + diff --git a/manuscript/About-the-Authors.md b/manuscript/About-the-Authors.md new file mode 100644 index 00000000..cd744d61 --- /dev/null +++ b/manuscript/About-the-Authors.md @@ -0,0 +1,7 @@ +# About the Authors + +{type: iframe, title:About the Authors, width:800, height:600, poster:resources/chapt_screen_images/about-the-authors.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/about-the-authors.html) + + + diff --git a/manuscript/About-this-Course.md b/manuscript/About-this-Course.md new file mode 100644 index 00000000..37769139 --- /dev/null +++ b/manuscript/About-this-Course.md @@ -0,0 +1,7 @@ +# About this Course + +{type: iframe, title:About this Course, width:800, height:600, poster:resources/chapt_screen_images/index.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/index.html) + + + diff --git a/manuscript/Book.txt b/manuscript/Book.txt new file mode 100644 index 00000000..02dc25bf --- /dev/null +++ b/manuscript/Book.txt @@ -0,0 +1,25 @@ +1-Introduction.md +2-A-Very-General-Genomics-Overview.md +3-Guidelines-for-Good-Metadata.md +4-Considerations-for-choosing-tools.md +5-General-Data-Analysis-Tools.md +6-Sequencing-Data.md +7-Microarray-Data.md +8-Annotating-Genomes.md +9-DNA-Methods-Overview.md +10-Whole-Genome-or-Exome-Sequencing.md +11-RNA-Methods-Overview.md +12-Bulk-RNA-seq.md +13-Single-cell-RNA-seq.md +14-Spatial-transcriptomics.md +15-Chromatin-Methods-Overview.md +16-ATAC-Seq.md +17-Single-cell-ATAC-Seq.md +18-ChIP-Seq.md +19-CUT&RUN-and-CUT&Tag.md +20-DNA-Methylation-Sequencing.md +21-Microbiome-Sequencing.md +22-ITCR--omic-Tool-Glossary.md +About-this-Course.md +About-the-Authors.md +References.md diff --git a/manuscript/References.md b/manuscript/References.md new file mode 100644 index 00000000..a89f3000 --- /dev/null +++ b/manuscript/References.md @@ -0,0 +1,7 @@ +# References + +{type: iframe, title:References, width:800, height:600, poster:resources/chapt_screen_images/references.png} +![](https://hutchdatascience.org/Choosing_Genomics_Tools/references.html) + + + diff --git a/manuscript/resources/chapt_screen_images/a-very-general-genomics-overview.png b/manuscript/resources/chapt_screen_images/a-very-general-genomics-overview.png new file mode 100644 index 00000000..fff72f66 Binary files /dev/null and b/manuscript/resources/chapt_screen_images/a-very-general-genomics-overview.png differ diff --git a/manuscript/resources/chapt_screen_images/about-the-authors.png b/manuscript/resources/chapt_screen_images/about-the-authors.png new file mode 100644 index 00000000..6eee60a7 Binary files /dev/null and b/manuscript/resources/chapt_screen_images/about-the-authors.png differ diff --git a/manuscript/resources/chapt_screen_images/annotating-genomes.png b/manuscript/resources/chapt_screen_images/annotating-genomes.png new file mode 100644 index 00000000..d0ff487f Binary files /dev/null and b/manuscript/resources/chapt_screen_images/annotating-genomes.png differ diff --git a/manuscript/resources/chapt_screen_images/atac-seq-1.png b/manuscript/resources/chapt_screen_images/atac-seq-1.png new file mode 100644 index 00000000..c8c0d05a Binary files /dev/null and b/manuscript/resources/chapt_screen_images/atac-seq-1.png differ diff --git a/manuscript/resources/chapt_screen_images/bulk-rna-seq-1.png b/manuscript/resources/chapt_screen_images/bulk-rna-seq-1.png new file mode 100644 index 00000000..d4aab838 Binary files /dev/null and b/manuscript/resources/chapt_screen_images/bulk-rna-seq-1.png differ diff --git a/manuscript/resources/chapt_screen_images/chip-seq-1.png b/manuscript/resources/chapt_screen_images/chip-seq-1.png new file mode 100644 index 00000000..50221b59 Binary files /dev/null and b/manuscript/resources/chapt_screen_images/chip-seq-1.png differ diff --git a/manuscript/resources/chapt_screen_images/chromatin-methods-overview.png b/manuscript/resources/chapt_screen_images/chromatin-methods-overview.png new file mode 100644 index 00000000..171d9d81 Binary files /dev/null and b/manuscript/resources/chapt_screen_images/chromatin-methods-overview.png differ diff --git a/manuscript/resources/chapt_screen_images/considerations-for-choosing-tools.png b/manuscript/resources/chapt_screen_images/considerations-for-choosing-tools.png new file mode 100644 index 00000000..13ee21dd Binary files /dev/null and b/manuscript/resources/chapt_screen_images/considerations-for-choosing-tools.png differ diff --git a/manuscript/resources/chapt_screen_images/cutrun-and-cuttag.png b/manuscript/resources/chapt_screen_images/cutrun-and-cuttag.png new file mode 100644 index 00000000..f14bc6cb Binary files /dev/null and b/manuscript/resources/chapt_screen_images/cutrun-and-cuttag.png differ diff --git a/manuscript/resources/chapt_screen_images/dna-methods-overview.png b/manuscript/resources/chapt_screen_images/dna-methods-overview.png new file mode 100644 index 00000000..e70cf761 Binary files /dev/null and b/manuscript/resources/chapt_screen_images/dna-methods-overview.png differ diff --git a/manuscript/resources/chapt_screen_images/dna-methylation-sequencing.png b/manuscript/resources/chapt_screen_images/dna-methylation-sequencing.png new file mode 100644 index 00000000..00a72e0f Binary files /dev/null and b/manuscript/resources/chapt_screen_images/dna-methylation-sequencing.png differ diff --git a/manuscript/resources/chapt_screen_images/general-data-analysis-tools.png b/manuscript/resources/chapt_screen_images/general-data-analysis-tools.png new file mode 100644 index 00000000..17b0ba77 Binary files /dev/null and b/manuscript/resources/chapt_screen_images/general-data-analysis-tools.png differ diff --git a/manuscript/resources/chapt_screen_images/guidelines-for-good-metadata.png b/manuscript/resources/chapt_screen_images/guidelines-for-good-metadata.png new file mode 100644 index 00000000..4d92b2c1 Binary files /dev/null and b/manuscript/resources/chapt_screen_images/guidelines-for-good-metadata.png differ diff --git a/manuscript/resources/chapt_screen_images/index.png b/manuscript/resources/chapt_screen_images/index.png new file mode 100644 index 00000000..4db51327 Binary files /dev/null and b/manuscript/resources/chapt_screen_images/index.png differ diff --git a/manuscript/resources/chapt_screen_images/introduction.png b/manuscript/resources/chapt_screen_images/introduction.png new file mode 100644 index 00000000..17a8e208 Binary files /dev/null and b/manuscript/resources/chapt_screen_images/introduction.png differ diff --git a/manuscript/resources/chapt_screen_images/itcr--omic-tool-glossary.png b/manuscript/resources/chapt_screen_images/itcr--omic-tool-glossary.png new file mode 100644 index 00000000..28148ecb Binary files /dev/null and b/manuscript/resources/chapt_screen_images/itcr--omic-tool-glossary.png differ diff --git a/manuscript/resources/chapt_screen_images/microarray-data.png b/manuscript/resources/chapt_screen_images/microarray-data.png new file mode 100644 index 00000000..274d236d Binary files /dev/null and b/manuscript/resources/chapt_screen_images/microarray-data.png differ diff --git a/manuscript/resources/chapt_screen_images/microbiome-sequencing.png b/manuscript/resources/chapt_screen_images/microbiome-sequencing.png new file mode 100644 index 00000000..c904dbb6 Binary files /dev/null and b/manuscript/resources/chapt_screen_images/microbiome-sequencing.png differ diff --git a/manuscript/resources/chapt_screen_images/references.png b/manuscript/resources/chapt_screen_images/references.png new file mode 100644 index 00000000..8a409df3 Binary files /dev/null and b/manuscript/resources/chapt_screen_images/references.png differ diff --git a/manuscript/resources/chapt_screen_images/rna-methods-overview.png b/manuscript/resources/chapt_screen_images/rna-methods-overview.png new file mode 100644 index 00000000..340812a0 Binary files /dev/null and b/manuscript/resources/chapt_screen_images/rna-methods-overview.png differ diff --git a/manuscript/resources/chapt_screen_images/sequencing-data.png b/manuscript/resources/chapt_screen_images/sequencing-data.png new file mode 100644 index 00000000..05a67450 Binary files /dev/null and b/manuscript/resources/chapt_screen_images/sequencing-data.png differ diff --git a/manuscript/resources/chapt_screen_images/single-cell-atac-seq-1.png b/manuscript/resources/chapt_screen_images/single-cell-atac-seq-1.png new file mode 100644 index 00000000..67901c10 Binary files /dev/null and b/manuscript/resources/chapt_screen_images/single-cell-atac-seq-1.png differ diff --git a/manuscript/resources/chapt_screen_images/single-cell-rna-seq.png b/manuscript/resources/chapt_screen_images/single-cell-rna-seq.png new file mode 100644 index 00000000..6379dfaf Binary files /dev/null and b/manuscript/resources/chapt_screen_images/single-cell-rna-seq.png differ diff --git a/manuscript/resources/chapt_screen_images/spatial-transcriptomics-1.png b/manuscript/resources/chapt_screen_images/spatial-transcriptomics-1.png new file mode 100644 index 00000000..53306d6b Binary files /dev/null and b/manuscript/resources/chapt_screen_images/spatial-transcriptomics-1.png differ diff --git a/manuscript/resources/chapt_screen_images/whole-genome-or-exome-sequencing.png b/manuscript/resources/chapt_screen_images/whole-genome-or-exome-sequencing.png new file mode 100644 index 00000000..3ac8681d Binary files /dev/null and b/manuscript/resources/chapt_screen_images/whole-genome-or-exome-sequencing.png differ