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CHANGELOG.md

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[2.2.2] - 2024-09-13

  • Added immunotherapy geneset to compute BCS of immunotherapy-related signatures.

[2.2.1] - 2024-02-20

  • Fixed dependency errors. Beyondcell requires Seurat >=4.0.0,<5.0.0 and Matrix ==1.6_1.1. Related to issue rgb(17, 85, 17).
  • Added Spatial Transcriptomics tutorial example.

[2.2.0] - 2023-07-06

  • Fixed an issue (#132) where bcScore's check for normalized data failed.
  • Fixed an issue (#135) where bcRanks was not computing the residual's mean.
  • Updated tutorials.
  • Removed bcRanks "general" statistics computation.
  • Removed GetStatistics function.

[2.1.0] - 2023-03-31

  • Fixed an error in bcClusters and bcSignatures when spatial = TRUE and images = NULL.
  • Fixed title error in bc4Squares. The current title matches the corresponding idents level.
  • Fixed error in bc4Squares when drug names were passed as topnames.
  • Updated pre-loaded collections, which have been trimmed to 250 up and 250 down genes.
  • Updated SSc collection, which only contains protein-coding genes.

[2.0.0] - 2023-01-25

  • Added functions to plot spatial transcriptomics data on top of selected images.
  • Added a function to load our collection of drug signatures: GetCollection.
  • Added a set of functional pathways related to cancer disease: these are available using include.pathways in GetCollection.
  • Added two new optional arguments to bc4Squares: x.cutoff and y.cutoff to set custom quadrant thresholds.
  • Added two new optional arguments to bcUMAP: npcs and seed to allow users to both set the number of components to compute in the PCA step and reproduce a given UMAP by specifying the seed.
  • Changed the KNN imputation methodology in bcRegressOut. Beyondcell now relies on DMwR instead of bnstruct.
  • Fixed multiple issues in the package when only a single signature was being provided by the user.
  • Updated the SSc collection. A previous source of drug signatures (CCLE) has been replaced by those from the PRISM study. CTRP and GDSC derived signatures have been updated to the latest releases of the aforementioned projects' data.
  • Updated the drug annotation to harmonize the mechanism of action for the compounds in the SSc collection.
  • Updated all of our pre-loaded collections, which are stored as geneset objects.
  • Updated GenerateGenesets to work on user-provided genesets stored in GMT format.
  • Updated beyondcell's dependencies.
  • Updated binned scales in bcSignatures to improve visualizations.
  • Removed the method argument from bcUMAP. Only the UWOT library implementation of UMAP is available.

[1.3.3] - 2022-01-12

  • Fixed an error in bcSubset when filtering by the proportion of NaN values. Previously, the beyondcell object wasn't a subset when using nan.sigs or nan.cells. Now those signatures/cells below or equal to the NaN threshold are kept. Related to issue #21.

[1.3.2] - 2021-12-20

  • Fixed an issue (#17) where if all the cells have a number of expressed genes < expr.thres, all the values for that signature will be NaN and so will be the switch point.

[1.3.1] - 2021-09-9

  • Added group annotation to rank tables: high/low/differential sensitivity is now defined for each tested drug.

[1.2.1] - 2021-06-29

  • Fixed an issue (#14) where bcSignatures would fail when used with pathways

[1.2.0] - 2021-06-8

  • Fixed an issue where bcMerge would fail if the background matrix was empty.

[1.1.1] - 2021-05-20

  • Updated pathways with the latest sources from MSigDB 7.3.
  • Added a directory called data-raw with both the code and the data used to generate the pathway signatures.

[1.1.0] - 2021-04-14

  • Added two new arguments in bcUMAP: method and return.model. method can be "umap-learn" or "uwot" (default). return.model is a logical argument that determines whether the function will return the uwot model (only valid when method = "uwot").
  • Changed tutorials: Typos have been corrected, chunks of code now specify the UMAP method ("umap-learn") and figures have been redrawn (they look the same as the originals).

[1.0.0] - 2021-04-8