rcannood/SCORPIUS issues and pull requests

#45 - "In the reduce_dimensionality function, is the first parameter 'expression' the normalized data or the original count data?"

Issue - State: open - Opened by LiuXinyuan6 about 2 months ago

#44 - Group_name factor conversion

Pull Request - State: open - Opened by asif7adil 6 months ago

#43 - vignette ‘seurat’ not found

Issue - State: open - Opened by JiahuaQu 6 months ago - 1 comment

#42 - Prepare for upcoming Seurat v5 release

Issue - State: open - Opened by saketkc about 1 year ago - 2 comments

#41 - Change color of trajectory path in draw_trajectory_plot

Issue - State: open - Opened by Safwat08 over 1 year ago

#40 - `reduce_dimensionality` on expression matrix filtered for highly variable genes?

Issue - State: open - Opened by lucygarner over 1 year ago - 1 comment

#39 - Error in array(ans, c(len.a%/%d2, d.ans), if (!is.null(names(dn.ans)) || : negative length vectors are not allowed

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

#38 - How to reverse the pseudotime？

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

#37 - Error in generating the "expression" object starting from Seurat object

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

#36 - group name error

Issue - State: open - Opened by CMSimpson8 over 2 years ago - 8 comments

#35 - Alternative to K-means clustering in infer_trajectory()

Issue - State: open - Opened by alikhuseynov almost 3 years ago

#34 - Input to reduce_dimensionality()/LMDS

Issue - State: open - Opened by lucygarner almost 3 years ago

#33 - Not enough memory at reduce_dimentionality step

Issue - State: open - Opened by alicekao1118 about 3 years ago - 2 comments

#32 - extract_modules() on larger objects

Issue - State: open - Opened by alikhuseynov about 3 years ago - 1 comment

#31 - Fix urls

Pull Request - State: closed - Opened by rcannood over 3 years ago

#30 - SCORPIUS 1.0.8

Pull Request - State: closed - Opened by rcannood over 3 years ago - 1 comment

#29 - Using tSNE cell embedding values for infer_trajectory

Issue - State: closed - Opened by chitopia over 3 years ago - 3 comments

#28 - SCTransform normalised data with SCORPIUS

Issue - State: closed - Opened by lucygarner almost 4 years ago - 3 comments

#27 - Can I use SCORPIUS with scATAC ?

Issue - State: closed - Opened by giovanegt almost 4 years ago - 4 comments

#26 - Understanding output of extract_modules() and comparability of gene importance scores between trajectories

Issue - State: closed - Opened by lucygarner almost 4 years ago - 5 comments

#25 - Any stochastic elements to SCORPIUS reduce_dimensionality() or infer_trajectory()

Issue - State: closed - Opened by lucygarner almost 4 years ago - 2 comments

#24 - Providing a custom color palette for row annotations in the draw_trajectory_heatmap function

Issue - State: closed - Opened by violehtone almost 4 years ago - 2 comments

#23 - Can Scorpius handle scaled residuals as input?

Issue - State: closed - Opened by violehtone almost 4 years ago - 2 comments

#22 - SCORPIUS 1.0.7

Pull Request - State: closed - Opened by rcannood over 4 years ago

#21 - meaningful of the trajectory direction

Issue - State: closed - Opened by sherriying over 4 years ago - 5 comments

#20 - SCORPIUS 1.0.6

Pull Request - State: closed - Opened by rcannood over 4 years ago

#19 - Revert the order of cells in draw_trajectory_heatmap

Issue - State: closed - Opened by lucygarner almost 5 years ago - 3 comments

#18 - Error when trying to change the colour for draw_trajectory_heatmap

Issue - State: closed - Opened by lucygarner almost 5 years ago - 2 comments

#17 - Run SCORPIUS on data with batch effects?

Issue - State: closed - Opened by lucygarner almost 5 years ago - 3 comments

#16 - Trajectory and Pseudotime on SEURAT v3 dataset

Issue - State: closed - Opened by DomenicoSkyWalker89 almost 5 years ago - 6 comments

#15 - Gene expression on trajectory plot

Issue - State: closed - Opened by lucygarner almost 5 years ago - 6 comments

#14 - Syntax issue on string 132

Pull Request - State: closed - Opened by kant over 5 years ago - 1 comment

#13 - Use continuous color gradient for points

Issue - State: closed - Opened by SteveBoothHLI over 5 years ago - 4 comments

#12 - Use discrete colormaps for plots

Issue - State: closed - Opened by siddharthst over 5 years ago - 4 comments

#11 - Bioconductor submission

Issue - State: open - Opened by robertamezquita over 5 years ago - 2 comments

#10 - Devel

Pull Request - State: closed - Opened by rcannood almost 6 years ago

#9 - reduce_dimensionality change

Issue - State: closed - Opened by anjanbharadwaj about 6 years ago - 4 comments

#8 - Refactor SCORPIUS code

Pull Request - State: closed - Opened by rcannood over 6 years ago - 1 comment

#7 - Update for princurve 2.0.2

Pull Request - State: closed - Opened by rcannood over 6 years ago - 1 comment

#6 - vignette

Issue - State: closed - Opened by baj12 over 7 years ago

#5 - Algorithm is slow in euclidean space!

Issue - State: closed - Opened by zouter almost 8 years ago

#4 - ginhoux.R

Issue - State: closed - Opened by doublehelixlf almost 8 years ago - 7 comments

#3 - Make k-means clustering optional

Issue - State: closed - Opened by rcannood over 8 years ago - 1 comment
Labels: enhancement

#2 - infer.trajectory throws exception when a data frame is passed

Issue - State: closed - Opened by rcannood over 8 years ago

#1 - draw.trajectory.heatmap does not accept a matrix

Issue - State: closed - Opened by zouter over 8 years ago - 2 comments

GitHub / rcannood/SCORPIUS issues and pull requests