CHANGES
=======

* link to biorxiv added
* link to biorxiv added
* minor updated to chromosome plot
* Minor analysis updates
* Mislabeled plots corrected
* Readme updated
* Readme updated
* Readme updated
* Readme updated
* AUC curves plots updated to take title as argument
* Readme updated
* Readme updated
* Readme updated
* test folder removed
* License updated
* Collateral essentiality analysis updated and simplified
* Enrichment AROCs swapped with rank AUCs
* Integration of meeting feedback. Added validations on the shRNA DRIVE data
* minor changes to generate manuscript figures
* Copy-number ratios in tumours
* Collateral essentialities analysis updated
* Analysis re-done using the re-annotated list of non-expressed genes
* Collateral essentialtiy analysis updated
* SVs analysis updated
* Small updates to qc bias assessment
* SVS correction updated
* correct svs bsub compatible
* Analysis re-ran
* File + folder paths aggregated in init file of scripts
* Project scripts refactored and exported
* deprecated analysis removed
* minor updates and reports folder removed from git
* SV plot updated
* segment size impact in ratio sv enrichment
* Ratio svs associations at segment level
* Plots aestetics updated
* Plots aestetics updated
* Functional analysis updated
* Regression metric added to GP bias correction
* colateral essentialities updated and svs chromosome plots
* colateral essentialities volcano
* colateral essentialities analysis filters updated
* Brass analysis integrated with crispy
* Sklearn deprecated y\_train\_mean corrected
* SVs correction with Crispy
* Crispy fitting with SVs
* Brass analysis updated
* SL plot layout updated
* SL analysis updated
* SV plot updated
* SVplot translocations updated
* SV plots updated
* MMR analysis updated
* Drug associations updated
* sv plot
* Updates in filtering drug-list
* Corrplot of robust associations
* Corrplot of robust associations
* signed interactions analysis added
* lm crispr-drug associations subset reverted to previous list
* Robust associations code refactored
* Linear regressions between drug and crispr code refactored. PPI assembly updated
* Drug linear correlations script updated with main
* Assemble of single aggent drug response data updated, mapping deprecated drug ids
* WGS Copy-number/CRISPR bias mapped
* copy-number ratio analysis updated. singed interaction analysis startedq
* MMR analysis updated
* Growth rate correlation with drug response PCA
* BRASS analysis updates
* Minor modifications to the bsub script of the copy-number correction
* .gitignore updated to not consider ChangeLog
* Copy-number correction bsub command updated
* Copy-number correction bsub command updated
* Copy-number bias correction script arguments updated
* CNV bias correction arguments updated
* CNV bin function uptaded to handle nans
* Collateral essentiality analysis refactored; bin\_cnv round bug fixed
* Copy-number ratios plots updated
* Copy-number bias per chromosome analysis added to qc and bias assessement
* Copy-number bias plotting of corrected crispr fold-changes updated
* QC and copy-number bias of original CRISPR fc plots updated
* Plotting main methods added
* Sample iteration fixed
* Assert bug corrected in cnv bias correction script
* Copy-number main bug fixed
* Deprecated Copy-number correction script removed
* Copy-number correction script main supports bsub
* Copy-number bed files processing main file updated
* Crispy refactoring main functions updated
* Var explained adapted to bias correction
* copy-number ratios script updated
* Crispy fold-change, correction and copy-number ratios scripts main method added
* Restructuring and FISH validation experiments
* Readme added to crispr scripts
* Crispy analysis re-factoring initiated
* Copy-number comparison between cripy estimated and picnic
* Copy-number comparison
* Gene copy-number ratio added; Copy-number matricies exported
* Copy-number estimations performed now at the segment bed file level
* WGS ploidy estimation comparison initiated
* Synthetic lethality analysis updated; SV analysis updated
* Synthetic lethality analysis updated
* Drug-CRISPR enrichment for significant associations
* SV brass updated
* Roc analysis done in the SV
* WGS structural variation analysis started
* Novel drug targets analysis updated
* Drug crispr associations updated
* Robust pharmacogenomic association analysis added
* PCA analysis of drug response data
* CRISPR Drug associations with genomic features added
* Drug crispr association plots updated
* Linear regressions r2 added for full model. Input data standardized
* Linear regression plots updated with newer analysis
* log ratio test added to linear regressions
* Output of linear regression formatted
* Linear regression added support to pandas dataframes
* Initial documentation added
* xrange modified to range
* Linear regression computational time optimisation
* Linear regression computational time optimisation
* Linear regression computational time optimisation
* Growth rate added as covariate for crispr versus drug association
* Kinship matrix with linear regression updated
* CRISPR/drug integration drug targets analysis
* CRISPR + drug response integration analysis
* Ratio implication in essential genes
* HaCaTs cell lines CRISPR; Correlation comparison CNV vs Ratio
* HaCaTs cell lines CRISPR; Correlation comparison CNV vs Ratio
* Systematic collateral essentialities focused on genes with high copy-number ratio and not expressed
* Systematic collateral essentialities analysis updated
* Copy-number ratios analysis refactored
* Copy-number ratio calculation exported to an independent script file
* Copy-number ratio calculation exported to an independent script file
* copy-number ratio effects minor updated testing other genomic features
* MRR pathway analysis samples updated
* MRR pathway analysis
* Ratio analysis performed with original fold-changes by feature
* Ratio analysis performed with original fold-changes
* Collateral essentiality updated
* Deprecated reports removed
* CRISPR variation across chromosome comments updated
* Bug fixed in chromosome copies estimation
* Set chromosome plot to comply with color palette
* CRISPR impact by chromosome analysis done
* Minor updated in plots layout
* Collateral essentialities analysis updated
* Collateral essentialities and copy-number ratio analysis updated
* Copy-number ratio analysis updated
* ploidy enrichment analysis
* Ploidy enrichment analysis
* CNV bias variation across cell lines
* Sample overall count and copy-number effect plots added
* Refactoring Crispy analysis scripts
* Synthetic lethalities analysis initiated
* Ploidy impact in CRISPR fold-change, linear regression
* Ploidy impact in CRISPR fold-change
* Metric plots adpated; CNV effect association with ploidy
* Copy-number ratio deprecated plots removed
* Copy-number ratio plots added
* Copy-number ratio association
* Copy-number ratio association with bias
* Synthetic lethal interactions with copy-number
* Synthetic lethal interactions with copy-number
* Karyotype analysis;Synthetic lethal
* Karyotype analysis
* Kinases phenotypic analysis updated
* kinases essentiality analysis started
* kinases essentiality corr
* kinases analysis started
* ccleanr comparison
* ccleanr comparison
* copy-number effect across cell lines reports
* copy-number effect across cell lines
* Benchmark plot updated
* Benchmark plot updated
* Assemble crispy corrected scores
* CCLE processing; GDSC+CCLE correction scripts added
* CCLE crispr data processed
* Processing GDSC completed
* Bias correction unsupervised and sample preprocessing
* Bias correction GP mean bug fixed; Model simplified to RBF
* Kernel benchamrk updated to unsupervised model
* kernel benchmark updated
* Kernel benchmark script added
* raw counts dropout metric
* copy-number impact variability
* Breast cell lines subtypes clustering
* Crispr + drug analysis updated and CERES comparison
* kmeans clustering updated
* Kmeans analysis to crispr + drug
* Reports updated. Crispr + drug analysis started
* Minor corrections added to biases correction module. Method comparison script added
* Multithreaded updated to run with concurrent futures
* Biases correction refactored to inherit GaussianProcessRegression
* deprecated plots removed. shrna benchmark added
* Crispy correction performed with CNV. Sampling of hyper parameters added
* Global analysis of GDSC CRISPR samples
* Fold-change correction performed with copy-number linear and non-linear
* Plot chromosome added; Variance explained exported
* Correction method refactored and scripts to execute in the cluster implemented
* Benchmark plots added
* DataMatrix class updated to process GDSC crispr panel
* Updates to DataMatrix class with processing methods
* package structured changed
* Source folder renamed
* Initial refactorisation of the package
* readme update
* readme update
* structure project updated
* shRNA comparison benchmark performed
* Comparison between CRISPR and shRNA
* crispy performed with linear and rbf regression
* Crispy ran with fold-changes calculated by crispy
* Optimisation performed with deseq fold-changes with lower bound estimated by out-of-sample prediction
* Gaussian fitting per gene
* Out-of-sampling prediction benchmark done
* GP updated to export standard errors
* Kernels hyperparameters updated
* normalisation and benchmark plots updated
* AROC analysis updated to consider only essential genes
* benchmark plots updated
* Benchmark functions separated from GP fitting
* Existing implementations ported
* Initial commit
