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Commits on Feb 26, 2024

• fix inferCNV for issue broadinstitute#342

  

  jade

  authored and

  jade

  committed
  a4f31ba

Commits on Dec 1, 2023

• Version bump to 1.19.1

  GeorgescuC

  committed
  cca1b6f

• Fix version number in latest NEWS

  GeorgescuC

  committed
  dc018d4

• Merge remote-tracking branch 'upstream/master'

  GeorgescuC

  committed
  72ad8cb

• Revert "Version bump to 1.17.1"

  Show description for 23e33ad
  GeorgescuC

  committed
  23e33ad

• Version bump to 1.17.1

  GeorgescuC

  committed
  45b1233

• Update NEWS file

  GeorgescuC

  committed
  edc7d79

• Update doc

  GeorgescuC

  committed
  9cf9bd3

Commits on Nov 29, 2023

• Transfer cluster_by_groups option to HMM when running in samples mode to allow running the HMM on "all_observations".

  GeorgescuC

  committed
  d019c20

• Add useRaster option to plot_per_group method and transfer it plot_cnv calls.

  GeorgescuC

  committed
  dc9a3c8

• Fix for plotting with dynamic_resolution enabled when the png size limit of cairo is hit to not have parts of the plot that try to be plotted outside the limit.

  GeorgescuC

  committed
  97d55a2

• New default setting for leiden_resolution now set to "auto" which will very roughly set a resolution value that scales with the number of cells to avoid over splitting subclusters when the number o…

  Show description for 8a46eaf
  GeorgescuC

  committed
  8a46eaf

Commits on Nov 28, 2023

• Update to work with Seurat v5 object changes.

  GeorgescuC

  committed
  7b8affc

Commits on Oct 24, 2023

• bump x.y.z version to odd y following creation of RELEASE_3_18 branch

  jwokaty

  committed
  db3a401

• bump x.y.z version to even y prior to creation of RELEASE_3_18 branch

  jwokaty

  committed
  f420cdc

Commits on May 29, 2023

• Allow i3 HMM to run without references, results will be based on all observations, so results will be relative to proportion of healthy to tumor cells.

  GeorgescuC

  committed
  f107733

Commits on May 24, 2023

• Fix typo in CLI script for one of the arguments.

  GeorgescuC

  committed
  270f045

• Change how the available number of cores is checked for random trees subclustering so that it checks against the max number of cores rather than what is defined by BIOCPARALLEL_WORKER_NUMBER which …

  Show description for 8c74854
  GeorgescuC

  committed
  8c74854

Commits on May 23, 2023

• Add a "no_" at the start of CLI script options that flip a boolean from a default TRUE to FALSE so that it is clearer that it disables the option.

  GeorgescuC

  committed
  4fd085a

• Update CLI script to have all options, new and older that just never got added to it.

  GeorgescuC

  committed
  9560309

Commits on Apr 25, 2023

• bump x.y.z version to odd y following creation of RELEASE_3_17 branch

  jwokaty

  committed
  5cf45f6

• bump x.y.z version to even y prior to creation of RELEASE_3_17 branch

  jwokaty

  committed
  2d89064

Commits on Mar 29, 2023

• Version bump to 1.15.3

  GeorgescuC

  committed
  445ebfd

• Update NEWS file

  GeorgescuC

  committed
  ac12e4d

Commits on Mar 24, 2023

• Link write_phylo option from run() to plot_cnv() calls.

  Show description for 52c6fec
  GeorgescuC

  committed
  52c6fec

• Merge branch 'test_fix_plot_recursion'

  GeorgescuC

  committed
  12a8d55

• Fully transfer subclustering information when running plot_per_group to each annotation's object to take advantage of subcluster being displayed on color bars now.

  GeorgescuC

  committed
  89186bd

Commits on Mar 23, 2023

• Add export of infercnv subclusters to Seurat object and features file generated by add_to_seurat.

  GeorgescuC

  committed
  3df65ad

Commits on Mar 22, 2023

• Now use the first of the 2 color bars on the left side of the observations heatmap to display subclusters when they have been calculated and k_obs_groups is not used (>1) when cluster_by_groups=F is.

  Show description for fb80c09
  GeorgescuC

  committed
  fb80c09

Commits on Mar 20, 2023

• Fix plot_subclusters() when using an object that was processed with cluster_by_groups=FALSE.

  GeorgescuC

  committed
  98d135d

• Fix for "meanvar" sim_method in hspike generation when there are no references and one of the observation annotations has only a single cell.

  GeorgescuC

  committed
  5a8a89b

Commits on Mar 8, 2023

• Version bump to 1.15.2

  GeorgescuC

  committed
  615520d

• Update NEWS file devel

  GeorgescuC

  committed
  06d54ad

• Update NEWS file

  GeorgescuC

  committed
  e2f21b9

Commits on Mar 3, 2023

• Added an option to plot subclusters automatically after subclustering steps. Default to True.

  GeorgescuC

  committed
  b379d12

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