00-cavadas-et-al-2016-supplements.md

Cavadas et al., Scientific Reports, 2016 Supplements

This gist pre-processes supplementary data from Cavadas et al. paper in Scientific Reports, citation below:

Cavadas, M.A.S., Mesnieres, M., Crifo, B., Manresa, M.C., Selfridge, A.C., Keogh, C.E., Fabian, Z., Scholz, C.C., Nolan, K.A., Rocha, L.M.A., et al. (2016). REST is a hypoxia-responsive transcriptional repressor. Sci Rep-Uk 6, 31355

Each of the notebooks downloads the data directly from the journal, converts it into an easier-to-work tsv format, and augments it with uniprot, ensembl and entrez identifiers.

The notebooks make extensive use of MyGene.info which can be cited as:

Xin, J., Mark, A., Afrasiabi, C., Tsueng, G., Juchler, M., Gopal, N., Stupp, G., Putman, T., Ainscough, B., Griffith, O., Torkamani, A., Whetzel, P., Mungall, C., Mooney, S., Su, A., Wu, C. (2016). High-performance web services for querying gene and variant annotation Genome Biology 17(1), 91. https://dx.doi.org/10.1186/s13059-016-0953-9

See individual notebooks for more info.

Cavadas et al., Scientific Reports, 2016 - Suppl. Table 1.ipynb

Cavadas et al., Scientific Reports, 2016 - Suppl. Table 3.ipynb

Cavadas et al., Scientific Reports, 2016 - Suppl. Table 5.ipynb

cavadas-et-al-2016-suppl-table-1-augmented.tsv

cavadas-et-al-2016-suppl-table-3-augmented.tsv

cavadas-et-al-2016-suppl-table-5-augmented.tsv

requirements.txt

matplotlib==3.4.1
mygene==3.2.2
numpy==1.20.2
pandas==1.2.3
seaborn==0.11.1
sinfo==0.3.1
tqdm==4.60.0
IPython==7.22.0
jupyter_client==6.1.12
jupyter_core==4.7.1
notebook==6.3.0
xlrd==2.0.1