Add jupyter notebooks for qPCR figures, culturing figures, qPCR limit…

… of detection and quantification (#6)

* jupyter notebooks for qPCR figures, culturing figures, qPCR limit of detection/quantification analysis

* dependencies

* move notebooks to their own directory

* no longer duplicate rows in metadata

* metadata changes

* increase font sizes, other small changes

environments/gut-to-soil-manuscript-figures-qiime2-tiny-2024.5.yml

@@ -1,11 +1,15 @@
 channels:
-- https://packages.qiime2.org/qiime2/2024.5/tiny/passed
-- https://packages.qiime2.org/qiime2/2024.5/amplicon/passed
-- conda-forge
-- bioconda
+  - https://packages.qiime2.org/qiime2/2024.5/tiny/passed
+  - https://packages.qiime2.org/qiime2/2024.5/amplicon/passed
+  - conda-forge
+  - bioconda
 dependencies:
   - qiime2-tiny
   - q2-diversity
   - pip
   - pip:
-    - gut_to_soil_manuscript_figures@git+https://github.com/caporaso-lab/gut-to-soil-manuscript-figures.git
+      - altair
+      - vl-convert-python
+      - openpyxl
+      - xlrd
+      - gut_to_soil_manuscript_figures@git+https://github.com/caporaso-lab/gut-to-soil-manuscript-figures.git