Oncoscan v1.3.1

Enhancement in function load_chas to accomodate for bug #3

(Will be version 1.4 in R/bioconductor 3.18)

Oncoscan v1.2

• Added two functions to handle ASCAT files instead of ChAS load_ascat and
  workflow_oncoscan.ascat.
• Main workflow function workflow_oncoscan.run is renamed
  workflow_oncoscan.chas for consistency with the ASCAT function
• Bug fixes in adjust_loh (crashed with segments of length 1 or if no LOH
  segments where present)
• Bug fix in script run_oncoscan_workflow.R

OncoscanR v1.1

What's new in v1.1

• To simplify the workflow, the gender of the patient is not taken into account
  anymore. That implies that in a male sample, a gain of 3 extra copies on the X
  or Y chromosome is considered as a gain and not an amplification anymore. For
  female samples, nothing changes.
• The oncoscan coverage has been corrected to reflect only areas where there are
  groups of probes. Isolated probes where causing issues to identify arm-level
  alterations as ChAS segments where never extended to these probes and the 90%
  threshold could never be met (particularly on chromosomal arms 9p and Yq).
• Minor corrections in vignette

OncoscanR v1.0

What's new in v1.0?

• The nLST test has been clinically validated on 384 patients from the PAOLA-1
  trial and the recommended threshold is now >=15.
• The default value for arm-level alterations has been set to 90% as mentioned
  in the publication [Christinat et al., J Mol Diagn 2021; PMID: 34454110].
• The genomic LOH score (percent of LOH bases) has been added; score_gloh.
• Adds a flag "low tumor?" in the oncoscan workflow if the percentage of altered bases is less than 1%.
• Package to be released on Bioconductor

OncoscanR v0.2.1

No novel functionalities.
Compatible with R 4.0.3 and GenomicRange 1.42.0 (BioConductor 3.12)

OncoscanR v0.2

Change to the HRD workflow with the use of the new nLST score (see .

OncoscanR v0.1

OncoscanR v0.1 with Myriad-like computation of HRD score. Use the file oncoscanR_0.1.0.tar.gz for installation in R.