Changelog

Source: NEWS.md

crumblr 0.99.22

• August 11, 2025
• update docs
• add fdr.cutoff argument to plotTreeTest() and `plotTreeTestBeta()

crumblr 0.99.21

• March 10, 2025
• address Bioc comments

crumblr 0.99.20

• March 10, 2025
• address Bioc comments

crumblr 0.99.19

• Feb 12, 2025
• address Bioc comments: https://github.com/Bioconductor/Contributions/issues/3699#issuecomment-2640806359

crumblr 0.99.17

• Feb 6, 2025
• address Bioc comments: https://github.com/Bioconductor/Contributions/issues/3699#issuecomment-2640806359

crumblr 0.99.13

• Jan 14, 2025
• Bioc submission

crumblr 0.99.11

• June 14, 2024
• improve documentation
• add plotForest()
• add standardize()

crumblr 0.99.10

• June 12, 2024
• add diffTree() and plotTreeTestBeta()
• regularize weight estimates

crumblr 0.99.9

• Feb 1, 2024
• add crumblr(..,method=method) for method %in% c("clr", "clr_2class")

crumblr 0.99.8

• May 12, 2023
• in treeTest() add argument shrink.cov = TRUE. This will give slightly different p-values, but protects against false positives when the number of features get large compared to the sample size

crumblr 0.99.7

• April 5, 2023
• fix plotting bug in plotTreeTest()

crumblr 0.99.6

• Dec 7, 2022
• update docs, add vignette, dependencies

crumblr 0.99.5

• Nov 29, 2022
• bug fix and update docs

crumblr 0.99.4

• enforce variancePartition version dependency

crumblr 0.99.3

• buildClusterTree() uses cosine distance by default
• treeTest() now uses method="treeTest" by default

crumblr 0.99.2

• update plotTreeTest()
• Use variancePartition dependency on GitHub

crumblr 0.99.1

• add functions to perform mvTest() on trees

crumblr 0.99.0

• Jun 24, 2022
• Fix version number for compatibility with Bioconductor

crumblr 1.0.7

• Feb 1, 2022
• fix vst()
• add plots plotScatterDensity() and meanSdPlot() for VST
• add vignette vst.Rmd

crumblr 1.0.6

• Jan 31, 2022
• add logo, example data

crumblr 1.0.5

• Dec 27, 2021
• add dmn.mle()
• use generic crumblr() function

crumblr 1.0.4

• Dec 23, 2021
• Update vignette
• export clr()

crumblr 1.0.3

• Dec 20, 2021
• fix vst bug

crumblr 1.0.2

• Dec 20, 2021
• add vst

crumblr 1.0.1

• Oct 29, 2021
• handle data.frame

crumblr 1.0.0

• Oct 28, 2021
• Initial version