PMID- 25061071
OWN - NLM
STAT- MEDLINE
DCOM- 20150109
LR  - 20211021
IS  - 1367-4811 (Electronic)
IS  - 1367-4803 (Print)
IS  - 1367-4803 (Linking)
VI  - 30
IP  - 21
DP  - 2014 Nov 1
TI  - FisHiCal: an R package for iterative FISH-based calibration of Hi-C data.
PG  - 3120-2
LID - 10.1093/bioinformatics/btu491 [doi]
AB  - The fluorescence in situ hybridization (FISH) method has been providing valuable 
      information on physical distances between loci (via image analysis) for several 
      decades. Recently, high-throughput data on nearby chemical contacts between and 
      within chromosomes became available with the Hi-C method. Here, we present 
      FisHiCal, an R package for an iterative FISH-based Hi-C calibration that exploits 
      in full the information coming from these methods. We describe here our 
      calibration model and present 3D inference methods that we have developed for 
      increasing its usability, namely, 3D reconstruction through local stress 
      minimization and detection of spatial inconsistencies. We next confirm our 
      calibration across three human cell lines and explain how the output of our 
      methods could inform our model, defining an iterative calibration pipeline, with 
      applications for quality assessment and meta-analysis. AVAILABILITY AND 
      IMPLEMENTATION: FisHiCal v1.1 is available from http://cran.r-project.org/.
CI  - (c) The Author 2014. Published by Oxford University Press. All rights reserved. For 
      Permissions, please e-mail: journals.permissions@oup.com.
FAU - Shavit, Yoli
AU  - Shavit Y
AD  - Computer Laboratory, University of Cambridge, Cambridge CB3 0FD and Cambridge 
      Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, UK.
FAU - Hamey, Fiona Kathryn
AU  - Hamey FK
AD  - Computer Laboratory, University of Cambridge, Cambridge CB3 0FD and Cambridge 
      Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, UK.
FAU - Lio, Pietro
AU  - Lio P
AD  - Computer Laboratory, University of Cambridge, Cambridge CB3 0FD and Cambridge 
      Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, UK.
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20140723
PL  - England
TA  - Bioinformatics
JT  - Bioinformatics (Oxford, England)
JID - 9808944
RN  - 0 (Chromatin)
SB  - IM
MH  - Calibration
MH  - Cell Line
MH  - Chromatin/*chemistry
MH  - Humans
MH  - Image Processing, Computer-Assisted
MH  - In Situ Hybridization, Fluorescence/*methods
MH  - K562 Cells
MH  - *Software
PMC - PMC4609013
EDAT- 2014/07/26 06:00
MHDA- 2015/01/13 06:00
PMCR- 2015/11/01
CRDT- 2014/07/26 06:00
PHST- 2014/07/26 06:00 [entrez]
PHST- 2014/07/26 06:00 [pubmed]
PHST- 2015/01/13 06:00 [medline]
PHST- 2015/11/01 00:00 [pmc-release]
AID - btu491 [pii]
AID - 10.1093/bioinformatics/btu491 [doi]
PST - ppublish
SO  - Bioinformatics. 2014 Nov 1;30(21):3120-2. doi: 10.1093/bioinformatics/btu491. 
      Epub 2014 Jul 23.