Ecosyste.ms: Issues

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

GitHub / digitalcytometry/cytospace issues and pull requests

#98 - Running cytospace with multiple slides

Issue - State: open - Opened by sharonlee7980 5 months ago - 1 comment

#97 - Cell Fraction estimation for Legacy ST with Smart-seq single-cell

Issue - State: closed - Opened by sahil-sahni 6 months ago - 11 comments

#96 - Is there a way to plot a specific celltype alone?

Issue - State: closed - Opened by NicolaasVanRenne 6 months ago - 1 comment

#95 - Error running cytoSPACE. glmGamPoi

Issue - State: closed - Opened by alfonsosaera 7 months ago - 4 comments

#94 - Integration error

Issue - State: closed - Opened by Ocean-Lyu 8 months ago - 3 comments

#93 - Guide post cytoSPACE

Issue - State: closed - Opened by xiweiwu 8 months ago - 2 comments

#92 - Any plans on updating working Python version?

Issue - State: closed - Opened by andrew-weisman 8 months ago - 2 comments

#91 - can i get the simulated dataset?

Issue - State: closed - Opened by jennyxxxxxx 9 months ago - 3 comments

#90 - Have Docker images or singularity images?

Issue - State: closed - Opened by caiquanyou 9 months ago - 1 comment

#89 - get_cellfracs_seuratv3 does not work on sparse matrix

Issue - State: open - Opened by smeiersab 9 months ago - 6 comments

#87 - glmGamPoi Error

Issue - State: closed - Opened by hannhat1998 9 months ago - 1 comment

#86 - Add glmGamPoi_1.2.0 to environment.yml

Pull Request - State: closed - Opened by WubingZhang 10 months ago

#85 - error, but I do not know why

Issue - State: closed - Opened by Yulintian 10 months ago - 2 comments

#84 - Update get_cellfracs_seuratv3.R

Pull Request - State: closed - Opened by WubingZhang 10 months ago

#83 - Working with Stereo-seq data

Issue - State: closed - Opened by tvegawaichman 11 months ago - 2 comments

#82 - Some cell types are not inferred

Issue - State: closed - Opened by fuerzhou 11 months ago - 4 comments

#81 - scRNA-seq reference

Issue - State: closed - Opened by ChenJin2020 11 months ago - 2 comments

#80 - color label for cellTypes

Issue - State: closed - Opened by abulislam 11 months ago - 1 comment

#79 - Error: Cannot find more nearest neighbours than there are points

Issue - State: closed - Opened by kwangdol 11 months ago - 1 comment

#78 - TypeError: '<' not supported between instances of 'str' and 'int' in plot.py

Issue - State: closed - Opened by suerle 12 months ago - 2 comments

#77 - run_cytospace Issue after successful install

Issue - State: closed - Opened by dmiyagi 12 months ago - 8 comments

#76 - OSError: Could not find 'spatial/tissue_positions_list.csv'

Issue - State: closed - Opened by gebdu about 1 year ago - 1 comment

#75 - comparing different dlides/sections

Issue - State: closed - Opened by gebdu about 1 year ago - 1 comment

#74 - possibility of sparse matrix support?

Issue - State: closed - Opened by mcaponegro about 1 year ago - 3 comments

#73 - Create releases for each version

Issue - State: closed - Opened by leej3 about 1 year ago - 3 comments

#72 - What's the reason of "Killed"?

Issue - State: closed - Opened by e-tomato about 1 year ago - 3 comments

#69 - Issues about parameter 'ctfep'

Issue - State: closed - Opened by wangzlgithub over 1 year ago - 3 comments

#67 - Running Error

Issue - State: closed - Opened by DHGK over 1 year ago - 4 comments

#66 - Segmentation fault error during linear assignment

Issue - State: closed - Opened by mcaponegro over 1 year ago - 2 comments

#65 - How to specify a 'genome' parameter?

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

#64 - can't install, plz help me

Issue - State: closed - Opened by wanglin1992 over 1 year ago - 1 comment

#63 - subprocess.CalledProcessError:

Issue - State: closed - Opened by trantunhi99 over 1 year ago

#62 - Simulated datasets

Issue - State: closed - Opened by jincanke over 1 year ago - 3 comments

#61 - Unexpected Terminated when Solving linear assignment problem

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

#60 - Denoising before running cytoSPACE

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

#59 - Purpose of single cell mode

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

#58 - TransferData failing with rare reference celltypes

Issue - State: closed - Opened by briglo over 1 year ago - 2 comments

#57 - Adding assay parameter to generate_cytospace_from_scRNA_seurat_object

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

#56 - Quick Gotchas and current solutions

Issue - State: closed - Opened by simoncmo over 1 year ago - 4 comments

#54 - cannot open file 'get_cellfracs_seuratv3.R

Issue - State: closed - Opened by gakabani over 1 year ago - 5 comments

#53 - Seurat_weights.txt does not exist

Issue - State: closed - Opened by williamsdrake over 1 year ago - 2 comments

#52 - Problem when cell_type_labels are numeric

Issue - State: closed - Opened by MostBeef over 1 year ago - 4 comments

#51 - Update for revision

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

#50 - RE: single cell reference

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

#49 - Update README.md

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#48 - Update README.md

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#47 - Update README

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#46 - Update generating from Seurat inputs section

Pull Request - State: closed - Opened by miladrafiee over 2 years ago

#45 - Update generating Seurat inputs section

Pull Request - State: closed - Opened by miladrafiee over 2 years ago

#44 - Updating generate CytoSPACE inputs from Seurat objects

Pull Request - State: closed - Opened by miladrafiee over 2 years ago

#43 - small update on ReadMe file

Pull Request - State: closed - Opened by miladrafiee over 2 years ago

#42 - Update data preparation files

Pull Request - State: closed - Opened by miladrafiee over 2 years ago

#41 - Update input file preparation

Pull Request - State: closed - Opened by miladrafiee over 2 years ago

#40 - Update CytoSPACE file preparation

Pull Request - State: closed - Opened by miladrafiee over 2 years ago

#39 - Updating plotting parameters

Pull Request - State: closed - Opened by miladrafiee over 2 years ago

#38 - update plotting section

Pull Request - State: closed - Opened by miladrafiee over 2 years ago

#37 - Update cytospace.py

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#36 - Update post_processing.py

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#35 - Update logging

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#34 - Update output code

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#33 - add a feature to plot non-Visium dimensions

Pull Request - State: closed - Opened by miladrafiee over 2 years ago

#32 - update plotting parameters

Pull Request - State: closed - Opened by miladrafiee over 2 years ago

#31 - Update README.md

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#30 - Update README.md

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#29 - add scripts to generate cytospace outputs

Pull Request - State: closed - Opened by miladrafiee over 2 years ago

#28 - Update README.md

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#27 - Update README.md

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#26 - Update argument_parser.py

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#25 - Update README.md

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#24 - Update solvers

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#23 - Update README.md

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#22 - Update README.md

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#21 - Update README.md

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#20 - Update README.md

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#19 - Update README.md

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#18 - Update README.md

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#17 - Update README.md

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#16 - Update README.md

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#15 - Update linear_assignment_solvers.py

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#14 - Update README.md

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#13 - Create environment_withlapjv.yml

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#12 - Update get_cellfracs_seuratv3.R

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#11 - Update README.md

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#10 - Add gdown instructions

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#9 - Include gdown in environment.yml

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#8 - updating plotting parameters

Pull Request - State: closed - Opened by miladrafiee over 2 years ago

#7 - optimizing plotting parameters

Pull Request - State: closed - Opened by miladrafiee over 2 years ago

#6 - Add arguments to be parsed from commandline

Pull Request - State: closed - Opened by cbsteen over 2 years ago

#5 - Update README.md

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#4 - Update description

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#3 - Update README with logo

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#2 - Add logo image

Pull Request - State: closed - Opened by erinlbrown over 2 years ago

#1 - update plotting function and ordering issue

Pull Request - State: closed - Opened by miladrafiee over 2 years ago