running publish gh-pages again

.quarto/cites/index.json

@@ -1 +1 @@
-{"single-cell.qmd":["scale.data"],"functional.qmd":[],"intro.qmd":["knuth84"],"3D.qmd":[],"references.qmd":[],"summary.qmd":[],"bulk.qmd":[],"resources.qmd":["Buffalo_2015"],"pipelines.qmd":["Buffalo_2015"],"index.qmd":["Buffalo_2015","scale.data","Buffalo_2015"]}
+{"intro.qmd":["knuth84"],"resources.qmd":["Buffalo_2015"],"functional.qmd":[],"single-cell.qmd":["scale.data"],"3D.qmd":[],"pipelines.qmd":["Buffalo_2015"],"summary.qmd":[],"index.qmd":["Buffalo_2015","scale.data","Buffalo_2015"],"bulk.qmd":[],"references.qmd":[]}

.quarto/xref/599d01af

@@ -1 +1 @@
-{"entries":[{"key":"sec-enrichment","caption":"3.2 Enrichment Analysis","order":{"section":[3,2,0,0,0,0,0],"number":1}}],"headings":["gene-name-conversions","sec-enrichment","overrepresention-analysis-ora","gene-set-enrichment-analysis-gsea"],"options":{"chapters":true}}
+{"options":{"chapters":true},"headings":["gene-name-conversions","sec-enrichment","overrepresention-analysis-ora","gene-set-enrichment-analysis-gsea"],"entries":[{"key":"sec-enrichment","caption":"3.2 Enrichment Analysis","order":{"section":[3,2,0,0,0,0,0],"number":1}}]}

.quarto/xref/6cb90168

@@ -1 +1 @@
-{"entries":[],"headings":["working-with-high-performance-computing-hpcs","environment-reproducibility","nextflow","the-command-line","one-liners","file-manipulation","unix-text-processing-awk-and-sed","miscellanous","working-with-lines","working-with-columns","working-with-strings","directories","alignment-files","bioinformatics-bits","getting-files-from-geo","making-ucsc-tracks","samtools","r-quirks"],"options":{"chapters":true}}
+{"headings":["working-with-high-performance-computing-hpcs","environment-reproducibility","nextflow","the-command-line","one-liners","file-manipulation","unix-text-processing-awk-and-sed","miscellanous","working-with-lines","working-with-columns","working-with-strings","directories","alignment-files","bioinformatics-bits","getting-files-from-geo","making-ucsc-tracks","samtools","r-quirks"],"options":{"chapters":true},"entries":[]}

.quarto/xref/7025cfa3

@@ -1 +1 @@
-{"entries":[],"headings":["resources","processing","downstream-analysis","ab-compartments","topological-associating-domain","loops","mustache","working-with-loops","apa","higlass","docker","resgen","navigating-higlass","ingesting-files-specifications","mcool","ab-compartments-1","tads","loops-1","chip-seq-and-atac-seq-tracks"],"options":{"chapters":true}}
+{"headings":["resources","processing","downstream-analysis","ab-compartments","topological-associating-domain","loops","mustache","working-with-loops","apa","higlass","docker","resgen","navigating-higlass","ingesting-files-specifications","mcool","ab-compartments-1","tads","loops-1","chip-seq-and-atac-seq-tracks"],"options":{"chapters":true},"entries":[]}

.quarto/xref/7a334c63

@@ -1 +1 @@
-{"headings":["rna-seq","differential-gene-expression","deciding-groups-and-plotting","chip-seq-and-atac-seq","spike-in-normalization","peak-calling","overlapping-peaks","motif-enrichment","plotting-heatmaps","genomic-annotation","sec-Bulk_Analysis"],"entries":[{"order":{"number":1,"section":[2,0,0,0,0,0,0]},"key":"sec-Bulk_Analysis"}],"options":{"chapters":true,"chapter-id":"sec-Bulk_Analysis"}}
+{"headings":["rna-seq","differential-gene-expression","deciding-groups-and-plotting","chip-seq-and-atac-seq","spike-in-normalization","peak-calling","overlapping-peaks","motif-enrichment","plotting-heatmaps","genomic-annotation","sec-Bulk_Analysis"],"options":{"chapters":true,"chapter-id":"sec-Bulk_Analysis"},"entries":[{"key":"sec-Bulk_Analysis","order":{"number":1,"section":[2,0,0,0,0,0,0]}}]}

.quarto/xref/b73c4d3c

@@ -1 +1 @@
-{"headings":["bioinformatics","programming","r","python","git","statistics","miscellanous"],"entries":[],"options":{"chapters":true}}
+{"headings":["bioinformatics","programming","r","python","git","statistics","miscellanous"],"options":{"chapters":true},"entries":[]}