NEWS.md

In peterawe/CMScaller: CMScaller: an R package for consensus molecular subtyping of colorectal cancer pre-clinical models

0.99.2

Changes

• genome annotations updated to GENCODE v26/genome build GRCh38.p10 (now reported as startup message)
• geneSets updated: MSigDB to v7.0 and reactome to download date 2019-Aug-22
• default heatmap colors changed to be less intrusive
• default qualitative color palette changed to Okabe & Ito's Color Universal Design

Features

• plotPC provides 2d visualization of PCA loadings

Bug fixes

• subCamera p-value legend lacked the color representing the highest value [reported by SH Moosavi]

Notes

• R 3.6.0 fixed a bug in sample(). Fix may break p-value reproducibility for older versions

0.99.1 (2019-August)

Scientific Reports publication

0.99.0

Scientific Reports resubmission

• license is now GPL v3.0
• documentation improved, more useful warnings added
• CMScaller default confidence threshold changed from p=0.1 to FDR=0.05
• CMScaller accepts HGNC symbols and Ensembl rownames (rowNames parameter)
• templates.CRIS added Isella CRIS-565 templates
• crcTCGAsubset now includes 92 instead of 80 samples
• replaceGeneId added for quick translation of matrix rownames
• geneSets.reactome added reactome gene sets with NCBI Entrez gene identifiers
• subPairs added for quick overview of templates-sample distances

0.1.0

initial submission

peterawe/CMScaller documentation built on June 13, 2020, 4:49 a.m.