Recurrence & Exponentials

Density-based clustering can use recurrent mutations.
Network-based clustering can use a new exponentials score for vertices.

v1.7.1

Bug fixes

Preprocess

• offset calculations - smarter PDB file parsing & corrected negative offsets
• archive extraction - fasta archive extraction order corrected (download if necessary then extract)

Main

• empty pair data - no more empty pair data files created if no pairs are found
• .siteroi - added the forgotten site-roi & site-cosmic pair data to search output
• site positions - sites only have 'start positions' that are the user given transcript position, without 'end positions' that were PDB positions

HotPho

Interesting residues (sites) can now be searched, clustered, and visualized.

Added Significance Module

v1.6.0

Adding Significance Module

Parallel structure-wise density-based clustering

v1.5.0

Addidng parallel clustering to the density module

Clustering for specific genes and structures

Added two new options allowing the user to provide a list of genes and/or a list of structures so that, the clustering will be performed only on the mutations that are from those genes and/or structures.

Support for GRCh38

Added capability to annotate transcript info using GRCh37 or GRCh38 along with any Ensembl release ranging from 55 to 87 (current as of mid Feb 2017).

v1.1.1

Adding structure-specific density-based clustering

Density

You can now cluster using a density-based approach.

Distances

Pairwise data can now be measured by the average point of two compounds instead of just the minimum distance between two constituent atoms. Distance cutoff defaults have been updated as well.