Capture Hi-C Analysis Engine

Toolkit for processing and calling interactions in capture Hi-C data. Converts BAM files into counts of reads linking restriction fragments, and identifies pairs of fragments that interact more than expected by chance. Significant interactions are identified by comparing the observed read count to the expected background rate from a count regression model.


News

chicane v0.1.0 2018-08-24

  • First CRAN release

chicane v0.0.3.3 2018-08-09

  • Remove restriction fragments from package
  • Slim down extdata folder

chicane v0.0.3.2 2018-06-28

  • Fix fill.in.zeros to replace NAs with zeros across all replicate columns

chicane v0.0.3.1 2018-06-19

  • Add adjustment.terms argument to allow user to adjust for covariates of their choice

chicane v0.0.3.0 2018-06-14

  • Support for parallel processing in cis-interactions model fitting

chicane v0.0.2.10 2018-04-30

  • Expanded test coverage, small code tweaks

chicane v0.0.2.9 2018-04-17

  • Added option for removing counts between adjacent restriction fragments
  • Fixed vignette to run without bedtools

chicane v0.0.2.8 2018-04-11

  • Move model fitting try-catch to helper function

chicane v0.0.2.7 2018-04-10

  • Option to store temporary files in specific directory

chicane v0.0.2.6 2018-03-19

  • Added convert.hicup.digest.bed helper function

chicane v0.0.2.5 2018-03-08

  • Vectorize get.id.components function

chicane v0.0.2.4 2018-03-06

  • Bugfix in get.id.components function

chicane v0.0.2.3 2018-03-02

  • Changes to pass CRAN checks
    • moved gamlss and gamlss.tr to Depends
  • Gracefully catch unknown errors

chicane v0.0.2.2 2018-03-01

  • refuse to proceed with data processing if intermediate files already exist
  • set data processing examples as \dontrun to get around bedtools dependency on CRAN
  • pass keep.files argument through chicane

chicane v0.0.2.1 2018-02-26

  • catch error if model fitting fails after warning

chicane v0.0.2.0 2018-02-15

  • minor test.enrichment bug fix
  • catch some --as-cran comments/ warnings
  • expanded test coverage

chicane v0.0.1.9 2018-02-14

  • Improvements to test.enrichment:
    • stratified sampling
    • exclude bait-to-bait by default
    • return results as data frame
    • consider proportion of total features
    • bugfixes

chicane v0.0.1.8 2018-02-13

  • Revamped data preparation step
  • fixed issue where keep.files was not passed through prepare.data

chicane v0.0.1.7 2018-02-12

  • Bare bones enrichment testing

chicane v0.0.1.6 2018-02-05

  • Graceful handling of glm.fitter errors
  • Added new level of verbosity

chicane v0.0.1.5 2018-02-02

  • Graceful handling of "no suitable coefficients found" errors
  • Pass starting values between distance bins when fitting model

chicane v0.0.1.4 2018-01-31

  • Retiring some TO DOs
  • Minor documentation tweaks

chicane v0.0.1.3 2018-01-30

  • Renamed package
  • Added tests for get.trans.count

Dudbridge v0.0.1.2 2018-01-24

  • Error/ warning catching for lack of overdispersion in data
  • Added epsilon parameter to be passed to GLM control objects

Dudbridge v0.0.1.1 2018-01-23

  • Switched from VGAM to GAMLSS for truncated distributions
  • Added truncated negative binomial
  • Added trace and maxit parameters to be passed to GLM/ GAMLSS control objects

Dudbridge v0.0.1.0 2018-01-19

  • Refactored to include run.model.fitting function
  • Removed more excess printing

Dudbridge v0.0.0.8 2018-01-19

  • Prettified verbose reports, removed excess printing
  • Added smart.split function and incorporated it into split.by.distance

Dudbridge v0.0.0.7 2018-01-18

  • Fixed bug in handling of distance.bins = 1
  • Switch to Poisson distribution when negative binomial fails to fit

Dudbridge v0.0.0.6 2018-01-17

  • Added truncated negative binomial distribution

Dudbridge v0.0.0.5 2018-01-15

  • Implemented filtering

Dudbridge v0.0.0.4 2018-01-12

  • Option to include zero counts in data (all or cis-only)
  • Minor bug fixes and sanity checks

Dudbridge v0.0.0.3 2018-01-09

  • Fixed trans count calculation

Dudbridge v0.0.0.2 2018-01-03

  • Removed other end adjustment from non bait-to-bait model

Reference manual

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install.packages("chicane")

0.1.1 by Erle Holgersen, 14 days ago


Browse source code at https://github.com/cran/chicane


Authors: Erle Holgersen [aut, cre] , Olivia Leavy [aut] , Olivia Fletcher [aut] , Frank Dudbridge [aut] , Syed Haider [aut]


Documentation:   PDF Manual  


GPL-2 license


Imports data.table, MASS, stats, foreach, doParallel, iterators

Depends on gamlss.tr, gamlss

Suggests knitr, rmarkdown, testthat, GenomicInteractions, Gviz, countreg

System requirements: bedtools


See at CRAN