Ecosyste.ms: Issues

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

GitHub / jianhuupenn/SpaGCN issues and pull requests

#88 - No spatial domain detected

Issue - State: closed - Opened by sang-15 7 months ago - 4 comments

#86 - SpaGCN's compatibility with mclust

Issue - State: open - Opened by rocketeer1998 8 months ago

#85 - How to run SpaGCN with histology as .png instead of .tif

Issue - State: closed - Opened by uthsavc about 1 year ago

#84 - Questions about the pancreatic cancer dataset

Issue - State: open - Opened by czwdcm about 1 year ago

#82 - module 'SpaGCN' has no attribute 'calculate_adj_matrix'

Issue - State: open - Opened by JavadP4 over 1 year ago - 1 comment

#81 - Update calculate_adj.py

Pull Request - State: open - Opened by ch1ru over 1 year ago

#80 - Performance without histology better than with histology

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

#79 - Please refer to igraph instead of python-igraph

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

#78 - BaseException: Could not construct partition: vector too long

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

#77 - Can't reproduce my results

Issue - State: open - Opened by yunbokai over 1 year ago - 3 comments

#76 - About modify coordinates

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

#75 - About the extended application of SpaGCN

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

#74 - Add GPU support

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

#73 - Variable names are not unique.

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

#71 - [Master_project] SpaGCN script

Pull Request - State: open - Opened by aleksa1902 over 1 year ago

#70 - Update util.py

Pull Request - State: open - Opened by zEpoch almost 2 years ago

#68 - The second part of the project

Pull Request - State: closed - Opened by aleksa1902 almost 2 years ago - 1 comment

#67 - Computation of q_ij

Issue - State: open - Opened by schae211 almost 2 years ago

#66 - Update setup.py

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

#65 - problem reproducing turtorial

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

#64 - High memory demands with large samples

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

#63 - Replace sklearn with scikit-learn dependency

Pull Request - State: closed - Opened by Zethson almost 2 years ago - 4 comments

#62 - Example data not available

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

#61 - How to choose radius for neighbouring domains?

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

#60 - Is it possible to run SpaGCN without histology image?

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

#59 - Update the virtual env python version

Pull Request - State: open - Opened by messcode almost 2 years ago

#58 - spatial location file

Issue - State: closed - Opened by YyLu5 about 2 years ago - 2 comments

#56 - The SLIDE-seq V2 data

Issue - State: open - Opened by uuup111 about 2 years ago

#55 - location file loss in old ST

Issue - State: closed - Opened by xiao-kong-long about 2 years ago - 1 comment

#54 - Batch effect issue for multiple 10X visium samples

Issue - State: open - Opened by archanabhardwaj over 2 years ago - 1 comment

#53 - AssertionError

Issue - State: open - Opened by yuchen345 over 2 years ago - 1 comment

#52 - About the rank_genes_groups function in utils.py

Issue - State: closed - Opened by LindsayMo over 2 years ago - 1 comment

#51 - how to use detect_spatial_domains_ez_mode without histology image

Issue - State: closed - Opened by linpei26 over 2 years ago - 2 comments

#49 - Adjacency matrix of DLPFC 151673

Issue - State: open - Opened by xiao-kong-long over 2 years ago - 3 comments

#48 - NotADirectoryError

Issue - State: closed - Opened by xiao-kong-long over 2 years ago - 2 comments

#47 - Error running spaGCN : Could not construct partition

Issue - State: closed - Opened by archanabhardwaj over 2 years ago - 3 comments

#45 - Reproduction issue on tutorial: error at the steps with louvain algorithm

Issue - State: closed - Opened by huimin230 over 2 years ago - 2 comments

#44 - Session crash on google colab

Issue - State: closed - Opened by shashkat over 2 years ago - 1 comment

#43 - Error at the steps with louvain algorithm

Issue - State: closed - Opened by avsarg over 2 years ago - 3 comments

#42 - How could I get the ground truth of GSE111672?

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

#41 - Student's t bug report

Issue - State: closed - Opened by tomo61098 over 2 years ago - 1 comment

#40 - target_cluster, x/y_pixel and nbr_domians in Identify SVGs section

Issue - State: closed - Opened by lifan18 over 2 years ago - 2 comments

#39 - How to use functions Moran_I and Geary_C ？

Issue - State: closed - Opened by QingJun3 over 2 years ago - 1 comment

#38 - A question about SpaGCN' data

Issue - State: closed - Opened by zhaofangyuan98 over 2 years ago - 1 comment

#37 - batch effect from ST data generated by multiple sequencing chips

Issue - State: closed - Opened by lifan18 over 2 years ago - 2 comments

#36 - calculation procedure exceeds maximum memory resource

Issue - State: closed - Opened by lifan18 over 2 years ago - 2 comments

#35 - Tutorial for imaging-based spatial data

Issue - State: closed - Opened by zhanglab2008 over 2 years ago - 3 comments

#34 - The problem of different results on DLPFC151673 data

Issue - State: closed - Opened by HappyLife-together over 2 years ago - 6 comments

#33 - AssertionError

Issue - State: closed - Opened by Qirongmao97 almost 3 years ago - 1 comment

#32 - A bug report

Issue - State: closed - Opened by tonyyang1995 almost 3 years ago - 1 comment

#31 - spg.calculate_adj_matrix is making all Nan with our own FFPE histology image

Issue - State: closed - Opened by galib36 almost 3 years ago - 7 comments

#30 - the mouse visual cortex STARmap data

Issue - State: closed - Opened by zzdj11 almost 3 years ago - 2 comments

#29 - Reproduction issue on tutorial

Issue - State: closed - Opened by JiayuanDing100 almost 3 years ago - 3 comments

#28 - Question about SpaGCN on reported datasets

Issue - State: closed - Opened by JiayuanDing100 almost 3 years ago - 2 comments

#27 - Bug report

Issue - State: closed - Opened by JiayuanDing100 almost 3 years ago - 1 comment

#26 - No module named 'scipy.linalg.cython_lapack'

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

#25 - Error during Run SpaGCN

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

#24 - Spatial domain information in the starMap dataset (Figure 6a)

Issue - State: closed - Opened by ciciQ777 about 3 years ago - 6 comments

#23 - Contradictory gene in meta gene

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

#22 - Unkown number of domains

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

#21 - cluster specific DEGs

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

#20 - 两组芯片合并后聚类问题（涉及批次效应）

Issue - State: closed - Opened by xiazhk163 about 3 years ago - 3 comments

#19 - running error

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

#18 - expression matrix for SpaGCN

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

#17 - n_clusters is not used in louvain initialization

Issue - State: closed - Opened by EdwardZhao1991 about 3 years ago - 1 comment

#16 - Link to download the ground truth

Issue - State: closed - Opened by JunMa11 about 3 years ago - 4 comments

#15 - Ground truth of case 151673

Issue - State: closed - Opened by JunMa11 about 3 years ago - 2 comments

#14 - Integrating consecutive slides

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

#13 - Annotate based on SpaGCN

Issue - State: closed - Opened by Yao-14 about 3 years ago - 1 comment

#11 - Using SpaGCN without image

Issue - State: closed - Opened by Yao-14 over 3 years ago - 3 comments

#10 - Generation of positions.txt

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

#9 - `TypeError` in `spg.find_meta_gene`

Issue - State: closed - Opened by Nick-Eagles over 3 years ago - 2 comments

#8 - `IndexError` in `spg.find_meta_gene`

Issue - State: closed - Opened by Nick-Eagles over 3 years ago - 6 comments

#7 - search_l gives None

Issue - State: closed - Opened by cnk113 over 3 years ago - 12 comments

#6 - Is it possible to use SpaGCN to integrate several datasets (slides)?

Issue - State: closed - Opened by JiaGuangshuai over 3 years ago - 2 comments

#5 - `n_clusters` does not always equal number of spatial domains found

Issue - State: closed - Opened by Nick-Eagles over 3 years ago - 2 comments

#4 - problem reproducing tutorial

Issue - State: closed - Opened by drighelli over 3 years ago - 7 comments

#3 - performance is not as good as shown in the tutorial?

Issue - State: closed - Opened by 21century-bio over 3 years ago - 2 comments

#2 - Minimal workflow to compute spatially variable genes

Issue - State: closed - Opened by davidecrs over 3 years ago - 7 comments