markdown source builds

Auto-generated via `{sandpaper}`
Source  : c7c884e
Branch  : main
Author  : Vini Salazar <17276653+vinisalazar@users.noreply.github.com>
Time    : 2026-06-05 02:56:23 +0000
Message : Merge pull request #7 from melbournebioinformatics/update/packages

Update 5 packages

Author: actions-user

config.yaml

@@ -0,0 +1,92 @@
+#------------------------------------------------------------
+# Values for this lesson.
+#------------------------------------------------------------
+
+# Which carpentry is this (swc, dc, lc, or cp)? < REPLACED with UNIMELB institutes >
+# uom: University of Melbourne
+# mb: Melbourne Bioinformatics
+# mig: Melbourne Integrative Genomics
+# wehi: Walter and Eliza Hall Institute
+carpentry: 'mb'
+
+# Alt-text description of the lesson.
+carpentry_description: 'Lesson Description'
+
+# Overall title for pages.
+title: 'Introduction to RNA-seq analysis'
+
+# Date the lesson was created (YYYY-MM-DD, this is empty by default)
+created: '2025-08-13'
+
+# Comma-separated list of keywords for the lesson
+keywords: RNA-seq, Biological replicates, Sequencing depth, Biological
+ variability, Technical replicates, RNA quality, Enrichment method, 
+ Experimental design
+
+# Life cycle stage of the lesson
+# possible values: pre-alpha, alpha, beta, stable
+life_cycle: 'alpha'
+
+# License of the lesson
+license: 'CC-BY 4.0'
+
+# Link to the source repository for this lesson
+source: 'https://github.com/melbournebioinformatics/intro-to-rna-seq'
+
+# Default branch of your lesson
+branch: 'main'
+
+# Who to contact if there are any issues
+contact: 'jiayi.si.2[ at ]unimelb.edu.au'
+
+# Navigation ------------------------------------------------
+#
+# Use the following menu items to specify the order of
+# individual pages in each dropdown section. Leave blank to
+# include all pages in the folder.
+#
+# Example -------------
+#
+# episodes:
+# - introduction.md
+# - first-steps.md
+#
+# learners:
+# - setup.md
+#
+# instructors:
+# - instructor-notes.md
+#
+# profiles:
+# - one-learner.md
+# - another-learner.md
+
+# Order of episodes in your lesson
+episodes:
+- introduction.Rmd
+- what-is-RNA-seq.Rmd
+- why-is-a-good-experimental-design-vital.Rmd
+- terminology.Rmd
+- the-importance-of-replicates-to-estimate-variance.Rmd
+- how-many-replicates-and-how-many-reads-do-I-need.Rmd
+- sequencing-options-to-consider.Rmd
+- summary.Rmd
+
+# Information for Learners
+learners:
+
+# Information for Instructors
+instructors:
+
+# Learner Profiles
+profiles:
+
+# Customisation ---------------------------------------------
+#
+# This space below is where custom yaml items (e.g. pinning
+# sandpaper and varnish versions) should live
+
+# This is the UoM varnish, which is a custom version of the Carpentries varnish
+varnish: 'melbournebioinformatics/uom-varnish@main'
+url: 'melbournebioinformatics.github.io/uom-varnish'
+