GitHub - hilaryjoyce/smfs-data-analysis

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 91 Commits
Cluster		Cluster
Coincidence		Coincidence
Density		Density
Extra_code		Extra_code
Transform		Transform
Tss_force		Tss_force
.gitignore		.gitignore
Adhesion peak.ipynb		Adhesion peak.ipynb
Checking BR parameters.ipynb		Checking BR parameters.ipynb
Coincidence_maxX.ipynb.orig		Coincidence_maxX.ipynb.orig
Force-Separation Analysis.ipynb		Force-Separation Analysis.ipynb
Force-Separation Clustering.ipynb		Force-Separation Clustering.ipynb
Multiple coincidence.ipynb		Multiple coincidence.ipynb
Neural Net.ipynb		Neural Net.ipynb
New Coincidence Matrix Saving.ipynb		New Coincidence Matrix Saving.ipynb
Persistence Length Effects.ipynb		Persistence Length Effects.ipynb
README		README
Subset_all_ala.ipynb		Subset_all_ala.ipynb
Thesis Figures Results - BR highc.ipynb		Thesis Figures Results - BR highc.ipynb
Thesis Figures Results - BR tf.ipynb		Thesis Figures Results - BR tf.ipynb
Thesis Figures Results - BR tf_c60.ipynb		Thesis Figures Results - BR tf_c60.ipynb
Thesis Figures Results - BR.ipynb		Thesis Figures Results - BR.ipynb
Thesis Figures Results - curvedc65.ipynb		Thesis Figures Results - curvedc65.ipynb
Thesis Figures Results - flatc50.ipynb		Thesis Figures Results - flatc50.ipynb
Thesis Figures Results - flatc65.ipynb		Thesis Figures Results - flatc65.ipynb
Thesis Figures Results - flatc65_nomixed.ipynb		Thesis Figures Results - flatc65_nomixed.ipynb
Thesis figures - Analysis Outline.ipynb		Thesis figures - Analysis Outline.ipynb
Thesis results - curved vs flat.ipynb		Thesis results - curved vs flat.ipynb
aLa_c27nm_old_fitting.ipynb		aLa_c27nm_old_fitting.ipynb
ala_all_sample_clustering.ipynb		ala_all_sample_clustering.ipynb
ala_curved_sample_clustering.ipynb		ala_curved_sample_clustering.ipynb
ala_flat_sample_clustering.ipynb		ala_flat_sample_clustering.ipynb
ala_flat_sample_force_clustering.ipynb		ala_flat_sample_force_clustering.ipynb
ala_flat_sample_minForce5.ipynb		ala_flat_sample_minForce5.ipynb
all_ala_curved_clustering.ipynb		all_ala_curved_clustering.ipynb
all_ala_flat_clustering.ipynb		all_ala_flat_clustering.ipynb
analysis_demo.ipynb		analysis_demo.ipynb
bacteriorhodopsin_analysis.ipynb		bacteriorhodopsin_analysis.ipynb
cluster testing.ipynb		cluster testing.ipynb
custom_clustering.ipynb		custom_clustering.ipynb
ipy_testing.ipynb		ipy_testing.ipynb
oligomer distribution.ipynb		oligomer distribution.ipynb

Repository files navigation

Here is all the code for analyzing both WLC-type data and peeling-type data.

Tss_force_code : 
    - takes raw data in Sara's form (DNA peeling data) and converts it to force vs. tip-sample-separation data
    - takes RDF files and converts them into tip-sample-separation data.

Peeling_code : 
    - takes peeling-type force-separation data and produces cut-off list of forces (2D -> 1D transform)

Transform_code : 
    - Lc_transform takes tss_force data and converts it using the WLC into Lc values (2D -> 1D transform)
    - Plateau_transform takes tss_force data and finds the last, long plateau as in DNA data and produces a list of those force values only

Density_code :
    - takes any list of values and produces a gaussian kernel density estimate

Coincidence_code :
    - takes any set of KDEs and calculates the coincidence matrix

Cluster_code :
    - takes any list representing a lower triangular coincidence matrix and produces an agglomerative hierarchical cluster