chicane v0.1.8 2021-11-03 -------------------------------------------------- * graceful handling of Gviz-UCSC error when retrieving chromosome lengths in vignettes when using R-4.1.0 chicane v0.1.7 2021-09-20 -------------------------------------------------- * enabling future compatability with data.table v1.14.2 by changing syntax names(data.table)['x' == names(data.table)] <- 'y' to setnames(data.table, 'x', 'y') chicane v0.1.6 2021-07-20 -------------------------------------------------- * updated vignettes' section: Pre-processing data to detail creation of baitmap and fragments files and brought the naming of files in sync with Nature Protocols' paper * fixed rare cases where scientific notations (e.g 1e10) were introduced in read.bed() * fixed a typo in vignettes: create.standard.format to convert.standard.format chicane v0.1.5 2021-06-08 -------------------------------------------------- * fixed prepare_bam.sh to make it work with all POSIX-compliant shells chicane v0.1.4 2021-03-17 -------------------------------------------------- * fixed rare cases where scientific notations were introduced in convert2bed leading to failure in bedr which treats it as a string (e.g 1e10) chicane v0.1.3 2020-09-19 -------------------------------------------------- * fixed a bug with first distance bin when it contained self-ligated interactions with distance=0 * added log-likelihood statistics to rootograms and saved model fit statistics chicane v0.1.2 2020-06-09 -------------------------------------------------- * added create.locus.plot function * added create.standard.format function * activated verbose statements * add replicate comparison chicane v0.1.1 2019-09-23 -------------------------------------------------- * improved memory handling * updated model definitions in the vignettes to match manuscript * add plots representing model fits against observed counts 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 chicane 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 chicane 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 chicane v0.0.1.0 2018-01-19 -------------------------------------------------- * Refactored to include run.model.fitting function * Removed more excess printing chicane v0.0.0.8 2018-01-19 -------------------------------------------------- * Prettified verbose reports, removed excess printing * Added smart.split function and incorporated it into split.by.distance chicane 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 chicane v0.0.0.6 2018-01-17 -------------------------------------------------- * Added truncated negative binomial distribution chicane v0.0.0.5 2018-01-15 -------------------------------------------------- * Implemented filtering chicane v0.0.0.4 2018-01-12 -------------------------------------------------- * Option to include zero counts in data (all or cis-only) * Minor bug fixes and sanity checks chicane v0.0.0.3 2018-01-09 -------------------------------------------------- * Fixed trans count calculation chicane v0.0.0.2 2018-01-03 -------------------------------------------------- * Removed other end adjustment from non bait-to-bait model