title: Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values.
abstract: CONCLUSIONS
  comb-p is a command-line tool and a python library that manipulates BED files of possibly irregularly spaced P-values and (1) calculates auto-correlation, (2) combines adjacent P-values, (3) performs false discovery adjustment, (4) finds regions of enrichment (i.e. series of adjacent low P-values) and (5) assigns significance to those regions. In addition, tools are provided for visualization and assessment. We provide validation and example uses on bisulfite-seq with P-values from Fisher's exact test, tiled methylation probes using a linear model and Dam-ID for chromatin binding using moderated t-statistics. Because the library accepts input in a simple, standardized format and is unaffected by the origin of the P-values, it can be used for a wide variety of applications.
  
  
  BACKGROUND
  comb-p is maintained under the BSD license. The documentation and implementation are available at https://github.com/brentp/combined-pvalues.
  
  
  BACKGROUND
  bpederse@gmail.com
authors.affiliation: Department of Medicine, University of Colorado, Denver, Anschutz Medical Campus, Aurora, CO 80045, USA. bpederse@gmail.com
authors.forename: Brent S
authors.initials: BS
authors.lastname: Pedersen
authors.forename: David A
authors.initials: DA
authors.lastname: Schwartz
authors.forename: Ivana V
authors.initials: IV
authors.lastname: Yang
authors.forename: Katerina J
authors.initials: KJ
authors.lastname: Kechris
mesh_terms: D015342:DNA Probes / Q000032:analysis / Q000235:genetics; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods*; D006801:Humans; D011381:Programming Languages; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D015342:DNA Probes