SARS-CoV-2-Data-Workflows

Work notebooks: jupyter notebooks for day-to-day SARS-CoV-2 data workflows

COVID-19 Symptoms abbreviations

Abbr	Symptom
GW	General (body) weakness/fatigue/malaise
FC	Fever/Chills
CO	Cough
ST	Sore throat
RN	Runny nose
SB	Shortness of breath/Difficulty in breathing
D	Diarrhoea
NV	Nausea/Vomiting
H	Headache
IC	Irritability/Confusion
P	Pain
LS	Loss of smell
LT	Loss of taste/appetite
P-M	Muscular pain
P-A	Abdominal pain
P-B	Back pain
P-C	Chest pain
P-J	Joint pain
BA	Body aches
SZ	Sneezing
HP	Hypertension
TN	Tonsillitis
DZ	Dizziness
NS	Night sweats

Name		Name	Last commit message	Last commit date
Latest commit History 127 Commits
README.md		README.md
aggregate-analysis-reports-nf-viralrecon.ipynb		aggregate-analysis-reports-nf-viralrecon.ipynb
analysis-notes.ipynb		analysis-notes.ipynb
avg_kit_coverage.png		avg_kit_coverage.png
avg_kit_coverage2.png		avg_kit_coverage2.png
cts-trends.ipynb		cts-trends.ipynb
generalised-seq-metadata-integration-and-KB.ipynb		generalised-seq-metadata-integration-and-KB.ipynb
gisaid_submissions.ipynb		gisaid_submissions.ipynb
metadata-cleaning.ipynb		metadata-cleaning.ipynb
retrieve-sapmles-cts.ipynb		retrieve-sapmles-cts.ipynb
sample-dualindexing.ipynb		sample-dualindexing.ipynb
track-spike-muts.ipynb		track-spike-muts.ipynb
trend-plots.ipynb		trend-plots.ipynb