Conos Versions Save

R package for the joint analysis of multiple single-cell RNA-seq datasets

v1.4.2

2 years ago

Version 1.4.2 published on CRAN, 29 June 2021

Changed

  • Add scaling to scaledMatricesSeurat(), scaledMatricesSeuratV3()
  • Change sccore::plapply() in updatePairs()

v1.4.1

3 years ago

Version 1.4.1 published on CRAN, 15 May 2021

Added

  • support Seurat objects in getOdGenesUniformly and con$correctGenes

Removed

  • functions collapseCellsByType and colSumByFactor are moved to sccore
  • removed strong dependency on drat repositories; only used now for the vignettes in the README

v1.4.0

3 years ago

Changed

  • extensive revisions for CRAN upload, including roxygen2 documentation
  • replaced relevant C++ code and Rcpp functions with N2R and leidenAlg
  • vignettes edits, detailing p2app4conos() for rendering Conos to pagoda2 application
  • updated Dockerfile
  • extensively revised vignettes and moved them, due to on CRAN build + check duration limits
  • README revisions for clarity

Added

  • added getGeneExpression() for Seurat v2 and v3 (January 2021)
  • add parameter raster.dpi in con$plotEmbedding() to replace raster.height and raster.width, given these parameters are defunct with *rewrite of ggrastr (v0.2.0)[https://github.com/VPetukhov/ggrastr/releases/tag/v0.2.0]
  • Rjnmf added as Rcpp function
  • auxiliary package conosPanel used

The initial CRAN version for conos 1.4.0 was published on Feb 23 2021: https://cran.r-project.org/web/packages/conos/index.html

v1.3.1

3 years ago

[1.3.1] - 2020-24-09

Changed

  • Improved plotDEheatmap function
  • Fixed bug with balancing.factor.per.sample in buildGraph
  • Fixed some installation problems
  • Improve R6 documentation
  • Installs on Mac OS

Added

  • Changed std::cout to Rcpp::Rcout (July 2020)
  • Revised README, vignettes (July 2020)
  • added ht_opt$message = FALSE for ComplexHeatmap (July 2020)
  • Added checks for getPerCellTypeDE() for errors, removing NAs (July 2020)
  • Added ht_opt$message = FALSE for ComplexHeatmap (July 2020)
  • Write to HDF5 for saveConosForScanPy() (July 2020)
  • LICENSE (July 2020)

Removed

  • Removed getCorrectionVector() and getPerCellTypeDECorrected (2 July 2020)
  • Removed all neighborhood averaging via neighborhood.average (4 July 2020)

v1.3.0-1

4 years ago

Tag to update the docker version build

v1.3.0

4 years ago

Changed

  • Moved some code to the new package sccore
  • Fixed inconsistent use of parameters for different spaces in buildGraph
  • Various small fixes
  • Fixed the number of components calculated for the simple PCA rotation
  • Conos is R6 class now (instead of refClass)

Added

  • Functionality for PAGA graph collapsing
  • Parameters k.same.factor and balancing.factor.per.sample to buildGraph. It can be used to improve alignment between different conditions: with same.factor.downweight it gives the system similar to k.self and k.self.weight
  • plotDEheatmap() function for viewing marker genes
  • Function convertToPagoda2 to create Pagoda 2 from Conos. Helpful for PagodaWebApp.

v1.2.1

4 years ago

Changed

  • Fixed getDifferentialGenes
  • Fixed testing clustering stability

v1.2.0

4 years ago

Changed

  • Added mean M value column to the diff. expression output
  • Optimized plotting with coloring by genes
  • getDifferentialGenes uses first clustering by default
  • Fixed bug with collapseCellsByType. Note: probably will affect DE results.
  • Added re-normalization of edge weights to fix problem with negative edge weights during label propagation
  • Now in plotting 'groups' aren't ignoted if 'gene' is provided: it's used to subset cells for plotting.
  • UMAP now set n_sgd_threads from uwot to n.cores by default. It gives much better parallelization, but kills reproducibility. Use n.sgd.cores=1 to get reproducible embeddings.
  • Account for target.dims in UMAP embedding
  • Fixed estimation of cor.based with alingnment.strength == 0. It removes edges with negative correlation and reduce down-weight of inter-sample edges, which can change results of the alignment.
  • Changed default value of fixed.initial.labels in propagateLabels from FALSE to TRUE. Presumably, FALSE should never be used.
  • New output format for label propagation (list of "labels", "uncertainty" and "label.distribution")
  • Numerous small bug fixes and small validations for correct arguments
  • ScanPy integration tutorials to refelect the changes in saveConosForScanPy

Added

  • Metrics to masure specifisity of cell type markers to DE info in getDifferentialGenes (parameters append.specifisity.metrics and append.auc)
  • Implementation of label propagateion based on matrix equations (occured to be too slow)
  • Function findSubcommunities to increase resolution for specific clusters
  • Parameter subgroups to embeddingPlot. It allows to plot only cells, belonging to the specified subgroups
  • Parameter keep.limits to embeddingPlot
  • Added metrics to masure specifisity of cell type markers to DE info in getDifferentialGenes (parameters append.specifisity.metrics and append.auc)
  • velocityInfoConos function for RNA velocity analysis on samples integrated with conos (together with supplementary functions prepareVelocity and pcaFromConos)
  • "Running RNA velocity on a conos object" section in README.md (explains usage of the velocityInfoConos function)
  • Function getJointCountMatrix to conos obect
  • New possibilities to customize the output of saveConosForScanPy
  • Function parseCellGroups to parse properly cell groupings depending on user settings
  • Function estimteWeightEntropyPerCell to visualize alignment quality per cell