References

Data and Code

Library	Version	Reference
RCC PE2	2016	Chen, Fengju et al. 2016. ‘Multilevel Genomics-Based Taxonomy of Renal Cell Carcinoma’. Cell Reports 14(10): 2476–89.
DESeq2	3.14	Love MI, Huber W, Anders S (2014). “Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.” Genome Biology, 15, 550. doi: 10.1186/s13059-014-0550-8.
GDC data portal	>= 1.0.1	See their documentation for citation at: https://gdc.cancer.gov/about-data/data-availability
TCGA, NIH	UI v1.25.1, API v3.0.0	Tomczak, K., Czerwińska, P., & Wiznerowicz, M. (2015). The Cancer Genome Atlas (TCGA): An immeasurable source of knowledge. Contemporary Oncology, 19(1A), A68–A77. https://doi.org/10.5114/wo.2014.47136
NumPy	>= 1.9.0	Harris, C.R., Millman, K.J., van der Walt, S.J. et al. Array programming with NumPy. Nature 585, 357–362 (2020). DOI: 0.1038/s41586-020-2649-2
tqdm	>= 4.31.0
pandas	>= 1.0.3
sciutil	>= 1.0.3
scibiomart	>= 1.0.1
sciviso	>= 1.0.1	https://github.com/ArianeMora/scidat
scidat	>= 1.0.1	https://github.com/ArianeMora/sciviso
Ensembl Biomart	Release 25	Sarah E Hunt, William McLaren, Laurent Gil, Anja Thormann, Helen Schuilenburg, Dan Sheppard, Andrew Parton, Irina M Armean, Stephen J Trevanion, Paul Flicek, Fiona Cunningham, Ensembl variation resources, Database Volume 2018, doi:10.1093/database/bay119

We strongly encourage you to cite the other packages, GDC data portal, and Ensembl databases

Environments

This will be user dependent but don’t forget to cite anaconda if you use it or reticulate if you use R.