stream_v1.1

What's Changed

• Fix incompatible issues related to the latest version of pandas by @huidongchen in #132
• Fix plotting issues related to the latest version of matplotlib and seaborn by @huidongchen in #133

Full Changelog: v1.0...v1.1

stream_v1.0

• added QC metrics and plots for both scRNA-seq and scATAC-seq
• added support of scATAC-seq analysis using peaks as features
• added support of interactive plots with plotly
• redesigned all plotting-related functions:
  • add figure setting function set_figure_params()
  • added support of visualization of multiple annotations
  • plot_branches_with_cells() has been integrated into plot_dimension_reduction()
  • subwaymap_plot() and subwaymap_plot_gene() have been integrated into a new function plot_stream_sc()
  • stream_plot() and stream_plot_gene() have been integrated into a new function plot_stream()
  • optimized the default settings of plotting functions
• redesigned mapping procedure
• added new function add save_vr_report() for singlecellVR website
• add exception handling for multiple functions
• fixed bugs
  add new parameter marker_list for marker detection functions

stream_v0.4.1

add support of top_pcs for mapping

stream_v0.4.0

• optimize marker gene detection
• add function set_workdir()
• add new parameters for command line
• add function add_metadata()
• add support of color range setting for gene plots
• add axis labels for UMAP and tSNE plots
• support removal of figure legends
• add auto detection of branching event for structure adjustment and plotting
• add the support of se for mapping
• add n_neighbors; nb_pct is deprecated
• change default dimension reduction to se;
• change default number of jobs to 1;
• change default value of loess_frac,min_num_cells,min_num_genes

stream_v0.3.9

Add the function find_marker() to find cell population specific markers

Update license, tutorials

stream_v0.3.8

Update MLLE by adding the support for different eigenvalue decomposition strategies based on the sample size
Change the default clustering method in seed_elastic_principal_graph() from affinity propagation to kmeans
Fix bugs in stream_plot() and stream_plot_gene()
Update tutorial 1

stream_v0.3.7

Add support for 10x Genomics Data
Add new function save_web_report() to generate the analysis report for visualization on STREAM website

stream_v0.3.6

Fix file path issue in command line interface

Add new parameters 'clustering' and 'n_clusters' in CLI

stream_v0.3.5

Fix plotting issues caused by matplotlib3

stream_v0.3.4

Update logarithm view of stream plots

Move single cell ATAC-seq preprocessing step to stream_atac package