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CLEAR Tools

Chromatin Landscape Exploration, Analysis, and Research Tools

Main Tools

APA2

Faster version of APA specifically for larger loop lists (>10k loops)

ATA:

Aggregate Track Analysis

FUSE

Combines multiple bedpe files into one. Flags available for duplicate removal, NMS, combining, and more. Attributes do not need to be in the same order between the files. Simplest usage is just to combine multiple bedpe files together without worrying about order of attributes etc.

SPLIT

Split up a bedpe into multiple lists. E.g. will split a file into 10 by randomly assigning features to 1 of the 10 outputs. Useful when you want to parallelize a task on a cluster but need to split up the bedpe to do it. Can use FUSE to combine the results into a final file. Specifying a number <= 0 will split the bedpe by chromosome (i.e. will make a new bedpe for each chromosome, and all features of that chromosome will be together in the split file)

INTERSECT

Intersect two bedpe files. Flag available to subtract the files instead of intersecting them. Also has flags for using exact matches, overlapping boundaries, etc.

EXPAND

Expands the size of anchors for each loop. Flags available for whether to explicitly set a size or only expand if the width is currently smaller than the requested width.

Dev or Deprecated Tools

PINPOINT

Peak Intensity (or Identification) Near Points Of INTeraction

FILTER

FLAGS

Focal Loop Aggregation via Grid Search

ENHANCE

Examining Neighborhoods at High-resolution by Aggregating Nearby Contact Events

old name: amplifi

Aggregating Mixed Peaks Leading to Improved Focal Intensity

RECAP

Ratios and Enrichments Compared Across Phenotypes

COMPILE

COMParing Interactions from Loops across Experiments

HOTSPOT

Highly Observable Transitions in Selective Pixels Of Tissues

SIFT

Search and Identify Focal Targets Simple Identification of Focal Targets

SIEVE

Selecting Interactions Enriched Versus Environment

SIMPLE

Simple Identification of Maximum Point of Local Enrichment

additional tools

probability

clean

CAMP Comparisons Across Multiple Phenotypes

ADAM analyze differences across maps

SLASH Summarizing Loop Aggregate Statistics and Hierarchies

TODO

ACE Annotating Cliques of Enrichment

CORE Cliques Of Regional Enrichments