Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / amc-heme/SCUBA issues and pull requests

#83 - fetch_reduction returns empty data.frame for SCE and anndata objects

Issue - State: open - Opened by wish1832 10 months ago
Labels: bug

#82 - gene_exists

Issue - State: open - Opened by wish1832 11 months ago

#81 - Add guidance on HDF5 compression in vignettes

Issue - State: open - Opened by wish1832 11 months ago

#80 - Update DESCRIPTION

Pull Request - State: closed - Opened by wish1832 about 1 year ago

#79 - Ci testing

Pull Request - State: closed - Opened by jairav about 1 year ago

#78 - Add Seurat license

Pull Request - State: closed - Opened by wish1832 about 1 year ago

#77 - Ci testing

Pull Request - State: closed - Opened by jairav about 1 year ago

#76 - catching up branch with additional_testing branch

Pull Request - State: closed - Opened by jairav about 1 year ago

#75 - Additional tests

Pull Request - State: closed - Opened by jairav about 1 year ago

#74 - Errors for unsupported uses of fetch_cells

Pull Request - State: closed - Opened by wish1832 about 1 year ago

#73 - Fix #71

Pull Request - State: closed - Opened by jairav about 1 year ago

#72 - Fix #71

Pull Request - State: closed - Opened by wish1832 about 1 year ago

#71 - Inconsistent behavior on FetchData for SCE objects

Issue - State: closed - Opened by jairav about 1 year ago
Labels: bug

#70 - SCUBA support for anndata objects

Pull Request - State: closed - Opened by wish1832 over 1 year ago

#69 - Error when calling plot_violin with a custom palette

Issue - State: open - Opened by wish1832 over 1 year ago
Labels: bug

#68 - split_by variable not properly processed via plot_violin

Issue - State: closed - Opened by wish1832 over 1 year ago
Labels: bug

#67 - Error in plot_violin when split_by is used

Issue - State: closed - Opened by wish1832 over 1 year ago
Labels: bug

#66 - Add fetch_matrix

Pull Request - State: closed - Opened by wish1832 over 1 year ago

#65 - Violin Plots: disable points for datasets with many cells

Issue - State: open - Opened by wish1832 over 1 year ago

#64 - Update anndata_fetchdata branch with renamed package references

Pull Request - State: closed - Opened by wish1832 over 1 year ago

#63 - Update anndata_fetchdata branch with name change to SCUBA

Pull Request - State: closed - Opened by wish1832 over 1 year ago

#62 - Rename Package to SCUBA in DESCRIPTION

Pull Request - State: closed - Opened by wish1832 over 1 year ago

#61 - Merge Updated Functions into Dev Branch

Pull Request - State: closed - Opened by wish1832 over 1 year ago

#60 - Merge pull request #59 from amc-heme/main

Pull Request - State: closed - Opened by jairav over 1 year ago

#59 - Anndata methods used in plot_reduction, tests

Pull Request - State: closed - Opened by jairav over 1 year ago

#58 - Differential Expression Function

Issue - State: open - Opened by wish1832 over 1 year ago

#57 - Anndata functions for plot reduction, including tests.

Pull Request - State: closed - Opened by jairav over 1 year ago

#56 - Error handling for fetch_metadata

Issue - State: closed - Opened by wish1832 over 1 year ago - 1 comment

#55 - Additional S3 Methods, changes to plotting functions

Pull Request - State: closed - Opened by wish1832 over 1 year ago

#54 - Custom ordering of groups

Issue - State: open - Opened by wish1832 over 1 year ago

#53 - Improper handling of non-existent reductions in reduction plot

Issue - State: open - Opened by wish1832 over 1 year ago
Labels: bug

#52 - Error in reduction plot for non-UMAP reductions

Issue - State: open - Opened by wish1832 over 1 year ago
Labels: bug

#51 - Pull full table with fetch_metadata

Pull Request - State: closed - Opened by wish1832 over 1 year ago

#50 - Metadata helper functions

Pull Request - State: closed - Opened by wish1832 over 1 year ago

#48 - Create function to display unique metadata values

Issue - State: open - Opened by wish1832 over 1 year ago

#47 - Dot and Scatterplot functions

Pull Request - State: closed - Opened by wish1832 over 1 year ago

#46 - Documentation: provide example code for each plotting function

Issue - State: open - Opened by wish1832 over 1 year ago
Labels: documentation

#45 - Method equivalent of WhichCells

Issue - State: open - Opened by wish1832 over 1 year ago - 2 comments

#44 - Violin and Ridge Plot Functions

Pull Request - State: closed - Opened by wish1832 over 1 year ago

#43 - Error with plot_violin function

Issue - State: closed - Opened by wish1832 over 1 year ago - 2 comments
Labels: bug

#42 - S3 Methods for object-specific code in ExIPlot

Issue - State: closed - Opened by wish1832 over 1 year ago - 1 comment

#41 - Update ViolinPlot branch with commits from main

Pull Request - State: closed - Opened by wish1832 over 1 year ago

#40 - Add ExIPlot Function

Issue - State: closed - Opened by wish1832 over 1 year ago - 1 comment

#39 - Add plot_feature

Pull Request - State: closed - Opened by wish1832 over 1 year ago

#38 - Add method to return default slot

Issue - State: closed - Opened by wish1832 over 1 year ago - 1 comment

#37 - Change "slot" to "layer" for FetchData

Issue - State: open - Opened by wish1832 over 1 year ago

#36 - DimPlot Performance Improvements

Pull Request - State: closed - Opened by wish1832 over 1 year ago

#35 - adds tests for shiny_stacked_bar. Resolves #34

Pull Request - State: closed - Opened by jairav almost 2 years ago

#34 - write tests for `shiny_stacked_bar`

Issue - State: closed - Opened by jairav almost 2 years ago

#33 - shiny pie test added. uses vdiffr.

Pull Request - State: closed - Opened by jairav almost 2 years ago

#32 - Update branch with latest version on main

Pull Request - State: closed - Opened by wish1832 almost 2 years ago

#31 - Method to identify default reduction

Issue - State: closed - Opened by wish1832 almost 2 years ago - 1 comment

#30 - Fixed shiny_pie bug(s) and bad roxygen export command

Pull Request - State: closed - Opened by jairav almost 2 years ago

#29 - FetchData does not pull reductions properly

Issue - State: closed - Opened by wish1832 almost 2 years ago - 1 comment
Labels: bug

#28 - Revise DimPlot function to use S3 methods

Issue - State: closed - Opened by wish1832 almost 2 years ago - 1 comment
Labels: enhancement

#27 - get_all_cells S3 method

Pull Request - State: closed - Opened by wish1832 almost 2 years ago

#26 - Create method to fetch all cells from an object

Issue - State: closed - Opened by wish1832 almost 2 years ago - 1 comment

#25 - Implement FetchData and other methods for CellDataSet

Issue - State: open - Opened by agillen almost 2 years ago
Labels: enhancement, low priority

#24 - Implement FetchData and other methods for anndata

Issue - State: open - Opened by agillen almost 2 years ago
Labels: enhancement

#23 - S3 methods for object-dependent plotting code outside of FetchData

Issue - State: open - Opened by wish1832 almost 2 years ago - 2 comments

#22 - FetchData with reductions

Pull Request - State: closed - Opened by wish1832 almost 2 years ago

#21 - Update branch with new commits from main

Pull Request - State: closed - Opened by wish1832 almost 2 years ago

#20 - Add violin plot function

Issue - State: closed - Opened by wish1832 almost 2 years ago - 2 comments

#19 - Add ridge plot function

Issue - State: closed - Opened by wish1832 almost 2 years ago - 3 comments

#18 - Add scatterplot function

Issue - State: open - Opened by wish1832 almost 2 years ago

#17 - Add dot plot function

Issue - State: open - Opened by wish1832 almost 2 years ago

#16 - Tests for FetchData with categorical metadata

Issue - State: open - Opened by wish1832 almost 2 years ago
Labels: Tests

#15 - Expand FetchData.SingleCellExperiment to pull reduction coordinates

Issue - State: closed - Opened by wish1832 almost 2 years ago - 2 comments

#14 - Test for FetchData

Pull Request - State: closed - Opened by wish1832 almost 2 years ago

#13 - Remove print statements from FetchData

Pull Request - State: closed - Opened by wish1832 almost 2 years ago

#12 - Shiny stacked bar

Pull Request - State: closed - Opened by jairav almost 2 years ago - 1 comment

#10 - R/shiny_pie.R completes issue #9

Pull Request - State: closed - Opened by jairav almost 2 years ago

#9 - Expand shiny_pie from scExploreR to operate on SingleCellExperiment objects.

Issue - State: closed - Opened by jairav almost 2 years ago
Labels: enhancement

#8 - Expand FetchData to return reduction coordinates

Issue - State: closed - Opened by wish1832 almost 2 years ago - 1 comment

#7 - Write tests for DimPlot function

Issue - State: open - Opened by wish1832 almost 2 years ago - 1 comment
Labels: Tests

#6 - Write tests for FetchData

Issue - State: closed - Opened by wish1832 almost 2 years ago - 1 comment
Labels: Tests

#5 - FetchData equivalent

Pull Request - State: closed - Opened by wish1832 almost 2 years ago

#4 - FetchData: handle error when a "slot" (assay) does not exist for an experiment

Issue - State: open - Opened by wish1832 almost 2 years ago - 1 comment
Labels: enhancement, Tests

#3 - Introduce testthat framework

Pull Request - State: closed - Opened by wish1832 almost 2 years ago

#2 - Add FetchData equivelent

Issue - State: open - Opened by wish1832 almost 2 years ago - 3 comments

#1 - Add FeaturePlot function for SCE objects

Issue - State: closed - Opened by wish1832 almost 2 years ago - 1 comment