Merge pull request #102 from AlexsLemonade/jaclyn-taroni/add-admin

Add administrative document; move code and data availability to methods

content/04.methods.md

@@ -164,3 +164,17 @@ Multiplexed libraries were not converted to `AnnData` objects, due to the potent
 All merged `SingleCellExperiment` objects were converted to `AnnData` objects and saved as `.hdf5` files.
 If a merged `SingleCellExperiment` object contained any ADT data, the RNA and ADT data were exported and saved separately as RNA (`_rna.hdf5`) and ADT (`_adt.hdf5`) objects.
 In contrast, if a merged `SingleCellExperiment` object contained HTO data due to the presence of any multiplexed libraries in the merged object, the HTO data was removed from the `SingleCellExperiment` object and not included in the exported `AnnData` object.
+
+## Code and data availability
+
+All summarized gene expression data and de-identified metadata are available for download on the ScPCA Portal, <https://scpca.alexslemonade.org/>.
+
+Documentation for the Portal can be found at <https://scpca.readthedocs.io>.
+
+All original code was developed within the following repositories and is publicly available as follows:
+
+- The `scpca-nf` workflow used to process all samples available on the Portal can be found at <https://github.com/AlexsLemonade/scpca-nf>.
+- The Single-cell Pediatric Cancer Atlas Portal code can be found at <https://github.com/AlexsLemonade/scpca-portal>.
+- Benchmarking of tools used to build `scpca-nf` can be found at <https://github.com/AlexsLemonade/alsf-scpca/tree/main/analysis> and <https://github.com/AlexsLemonade/sc-data-integration/tree/main/celltype_annotation>.
+- All code for the underlying figures can be found at <https://github.com/AlexsLemonade/scpca-paper-figures>.
+- The manuscript can be found at <https://github.com/AlexsLemonade/ScPCA-manuscript>.

content/06.administrative.md

@@ -0,0 +1,15 @@
+## Acknowledgments
+
+We thank the data generators and submitters of the Single-cell Pediatric Cancer Atlas.
+
+This work was funded through the Alex's Lemonade Stand Foundation Childhood Cancer Data Lab and Childhood Cancer Data Lab Postdoctoral Fellowship (SMF).
+
+## Author Contributions
+
+|Author|Contributions|
+|---|---|{% for author in manubot.authors %}
+|{{author.name}}|{% if author.contributions is string %}{{author.contributions}}{% else %}{% for contribution in author.contributions %}{{ contribution }}{% if not loop.last %}, {% endif %}{% endfor %}{% endif %}|{% endfor %}
+
+## Declarations of Interest
+
+AGH, JAS, SJS, DSM, DVP, NI, AY, KGW, CJB, JO, and JNT are or were employees of Alex's Lemonade Stand Foundation, a sponsor of this research.