rajewsky-lab/novosparc issues and pull requests

#65 - `plot_transport_entropy_dist` without atlas

Pull Request - State: open - Opened by rvinas over 1 year ago

#64 - feature gaussian cleanup

Pull Request - State: open - Opened by vfschumann about 2 years ago - 1 comment

#63 - Reference atlas creation

Issue - State: open - Opened by liliay almost 3 years ago - 1 comment

#62 - How to create the tissue.png file

Issue - State: open - Opened by liliay almost 3 years ago - 1 comment

#61 - No attribute "io" - Input data import

Issue - State: closed - Opened by Diennguyen8290 almost 3 years ago

#60 - error when running tissue.setup_reconstruction

Issue - State: closed - Opened by shermas about 3 years ago - 8 comments

#59 - Values for ref atlas

Issue - State: closed - Opened by shermas about 3 years ago - 1 comment

#58 - how can I save a tissue object

Issue - State: closed - Opened by shermas about 3 years ago - 1 comment

#57 - getting original cell identities with target space locations

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

#56 - visualizing gene expression in multiple slices or 3D

Issue - State: open - Opened by shermas about 3 years ago - 5 comments

#55 - importing tiff stack for target space

Issue - State: open - Opened by shermas about 3 years ago

#54 - novosparc exhausts memory when anndata.X in sparse matrix format (CSC or CSR)

Issue - State: open - Opened by sztankatt about 3 years ago

#53 - Question: Use of novosparc on tumor samples

Issue - State: closed - Opened by ccruizm about 3 years ago - 2 comments

#52 - novosparc fails (exit 137, process killed)

Issue - State: closed - Opened by dawe over 3 years ago - 5 comments

#51 - add missing import

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

#50 - division by zero error 'sinkhorn' optimization

Issue - State: open - Opened by zoepiran over 3 years ago

#49 - minor bug fix

Pull Request - State: open - Opened by nukappa over 3 years ago - 1 comment

#48 - Question about implementation and input data

Issue - State: open - Opened by s849 over 3 years ago

#47 - Display of ubiquitous genes

Issue - State: closed - Opened by MalteMederacke almost 4 years ago - 1 comment

#46 - Reconstruction with Marker Warning

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

#45 - Update dependencies

Issue - State: closed - Opened by MalteMederacke almost 4 years ago - 1 comment

#44 - output problem

Issue - State: closed - Opened by caiquanyou about 4 years ago - 3 comments

#43 - Atlas Matrix Bug

Issue - State: closed - Opened by mjang2000 about 4 years ago - 8 comments

#42 - Possibility to extract mapping information of cell to location in geometry?

Issue - State: closed - Opened by Hsu-Che-Wei about 4 years ago - 2 comments

#41 - The global transformation use in de novo reconstruction of Drosophila sc RNA-seq data

Issue - State: closed - Opened by hebeishangjiang about 4 years ago

#40 - Updates with anndata, geometries, project structure

Pull Request - State: closed - Opened by enessenel about 4 years ago

#39 - Plot positional confidences

Issue - State: closed - Opened by MalteMederacke about 4 years ago - 3 comments

#38 - How to generate the space information for the reference marker genes

Issue - State: closed - Opened by MinjieHu over 4 years ago - 8 comments

#37 - Downsampling of locations

Issue - State: closed - Opened by MalteMederacke over 4 years ago - 2 comments

#36 - /novosparc/plotting/_plotting.py

Issue - State: closed - Opened by WhatAboutMyStar over 4 years ago - 2 comments

#35 - Create new spatial markes from ISH images

Issue - State: closed - Opened by MalteMederacke over 4 years ago - 2 comments

#34 - Repeatability

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

#33 - Implemented moran's i and removed pysal from dependencies

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

#32 - import novosparc error

Issue - State: closed - Opened by zhangbaso over 4 years ago

#31 - How to plot two or more genes in the same time?

Issue - State: closed - Opened by YiweiNiu over 4 years ago - 2 comments

#30 - Can we get the relative distance of all cells?

Issue - State: closed - Opened by YiweiNiu over 4 years ago - 3 comments

#29 - Full environment and version

Issue - State: closed - Opened by HichamAffia over 4 years ago - 3 comments

#28 - ModuleNotFoundError: No module named 'pysal.explore.esda'

Issue - State: closed - Opened by I-Hao over 4 years ago - 2 comments

#27 - Unable to run sample files

Issue - State: closed - Opened by YvonneChenCS over 4 years ago - 2 comments

#26 - About mouse cerebellum slices data

Issue - State: closed - Opened by tauhidstanford over 4 years ago

#25 - Installation issues

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

#24 - Moran's I implementation for spatially informative genes

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

#23 - bdtnp.txt file missing

Issue - State: closed - Opened by HichamAffia over 4 years ago - 1 comment

#22 - The object hold Moran’s score

Issue - State: closed - Opened by I-Hao over 4 years ago - 2 comments

#21 - Some fixes to reconstruction examples, reconstruction notebook figures still wrong

Pull Request - State: closed - Opened by patrickaoude almost 5 years ago

#20 - nc.rc.setup_for_OT_reconstruction

Issue - State: closed - Opened by kzxkzx almost 5 years ago - 1 comment

#19 - geometry.txt

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

#18 - bdtnp.txt

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

#17 - added missing data for Drosophila scRNAseq

Pull Request - State: closed - Opened by nukappa almost 5 years ago

#16 - Files not found

Issue - State: closed - Opened by tauhidstanford almost 5 years ago - 1 comment

#15 - How to calculate D(exp, phys)?

Issue - State: closed - Opened by ChengxiangQiu almost 5 years ago - 1 comment

#14 - Added tutorial for reconstructing the Drosophila embryo

Pull Request - State: closed - Opened by nukappa almost 5 years ago

#13 - problem with create_target_space_from_image() function

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

#12 - Added function for constructing target spaces from an image

Pull Request - State: closed - Opened by nukappa almost 5 years ago

#11 - Different grids shapes and spatially informative genes

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

#10 - Can you show us a much more detailful vignette from 10X datasets?

Issue - State: closed - Opened by pangxueyu233 almost 5 years ago - 9 comments

#9 - Release notes for 0.3.7

Pull Request - State: closed - Opened by nukappa about 5 years ago