seqwalk paper reproducibility

This repository contains the code necessary to reproduce results from the paper. For the seqwalk software library, see here.

Some potentially helpful tips

DeLOB_benchmarks.ipynb contains the code for our reimplementation of DeLOB, and our benchmarking presented in Figure 2.
Supplementary notes 4-6 contain analyses of many SeqWalk generated libraries. Rather than including all 11 million sequences in the repository, we instead include library_generation.ipynb, which is a self-contained notebook that will generate all necessary libraries, which can then be analysed by gc_content.ipynb, melting_temp.ipynb, secondary_struct.ipynb

Name		Name	Last commit message	Last commit date
Latest commit History 13 Commits
qcbc		qcbc
.DS_Store		.DS_Store
.gitignore		.gitignore
DeLOB_benchmarking.csv		DeLOB_benchmarking.csv
DeLOB_benchmarking_pretty_plots.ipynb		DeLOB_benchmarking_pretty_plots.ipynb
DeLOB_benchmarks.ipynb		DeLOB_benchmarks.ipynb
DeLOB_sequence_identity.ipynb		DeLOB_sequence_identity.ipynb
EF1_sn4.pdf		EF1_sn4.pdf
EF2_sn5.pdf		EF2_sn5.pdf
EF3_sn6.pdf		EF3_sn6.pdf
EF4_sn7.pdf		EF4_sn7.pdf
EF5_sn9.pdf		EF5_sn9.pdf
EF6_sn10.pdf		EF6_sn10.pdf
EF7_sn10.pdf		EF7_sn10.pdf
README.md		README.md
constrained_library_sizes.csv		constrained_library_sizes.csv
f2.pdf		f2.pdf
gc_content.ipynb		gc_content.ipynb
gc_contents.csv		gc_contents.csv
library_generation.ipynb		library_generation.ipynb
melting_temp.ipynb		melting_temp.ipynb
melting_temps.csv		melting_temps.csv
pattern_removal.ipynb		pattern_removal.ipynb
pffe_analysis.ipynb		pffe_analysis.ipynb
qcbc.ipynb		qcbc.ipynb
secondary_struct.ipynb		secondary_struct.ipynb
secondary_structs.csv		secondary_structs.csv
seqwalk_25mer_benchmark.csv		seqwalk_25mer_benchmark.csv
seqwalk_25mers_benchmark.ipynb		seqwalk_25mers_benchmark.ipynb
source_data_f2.csv		source_data_f2.csv
ssm_vs_deltaG.ipynb		ssm_vs_deltaG.ipynb