Ecosyste.ms: Issues

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GitHub / mahmoodlab/hest issues and pull requests

#73 - Make HEST-Benchmark deterministic

Pull Request - State: closed - Opened by guillaumejaume 5 days ago

#72 - HEST installation on Windows fails with missing wheel error

Issue - State: closed - Opened by adiv5 7 days ago - 2 comments
Labels: installation

#71 - HESTData: provide util to map ensemble ID to gene name

Pull Request - State: closed - Opened by konst-int-i 9 days ago - 3 comments
Labels: enhancement

#70 - Mapping gene names to Ensembl IDs

Issue - State: open - Opened by JosephDiPalma 13 days ago - 3 comments
Labels: enhancement

#69 - add dask suppport and valis alignment

Pull Request - State: closed - Opened by pauldoucet 13 days ago

#68 - Inconsistent samples between HEST-1k and HEST-bench

Issue - State: closed - Opened by huangtinglin 13 days ago - 4 comments

#67 - Xenium transcripts single-cell data analysis

Issue - State: closed - Opened by Arkkienkeli 14 days ago - 2 comments

#66 - Update README.md

Pull Request - State: closed - Opened by guillaumejaume 16 days ago

#65 - Guillaumejaume patch 1

Pull Request - State: closed - Opened by guillaumejaume 17 days ago

#64 - Updated figure flipped species counts

Issue - State: closed - Opened by JosephDiPalma 18 days ago - 1 comment

#63 - HESTData: update `to_spatial_data()```

Pull Request - State: closed - Opened by konst-int-i 20 days ago - 3 comments
Labels: bug, enhancement

#61 - How to use Xenium data for cell segmentations?

Issue - State: closed - Opened by schoonhovenrichard 21 days ago - 4 comments

#60 - Regarding the Number of Patches and Spots in Xenium Dataset

Issue - State: closed - Opened by Yoyiming 25 days ago - 2 comments

#58 - Update README.md

Pull Request - State: closed - Opened by guillaumejaume 28 days ago

#57 - Patches not normalized by pixel size

Issue - State: closed - Opened by yijiangchen about 1 month ago - 6 comments

#56 - Missing Data in Xenium "transcripts/" Folder?

Issue - State: closed - Opened by sky-lzy about 1 month ago - 3 comments

#55 - Questions about image cropping

Issue - State: closed - Opened by HelloWorldLTY about 1 month ago - 2 comments

#54 - Number of cells in human xenium samples

Issue - State: closed - Opened by kotr98 about 2 months ago - 3 comments

#53 - add new samples and aligned transcripts

Pull Request - State: closed - Opened by pauldoucet about 2 months ago

#51 - One Xenium dataset on human breast cancer not in the database

Issue - State: closed - Opened by kennethahah 2 months ago - 3 comments

#50 - Reproduce benchmark results

Issue - State: closed - Opened by judyueshen 2 months ago - 5 comments

#49 - Refactor readthedocs

Pull Request - State: closed - Opened by pauldoucet 2 months ago

#48 - Update 4-Running-HEST-Benchmark.ipynb

Pull Request - State: closed - Opened by guillaumejaume 2 months ago

#47 - About patches in WSI

Issue - State: closed - Opened by Yoyiming 2 months ago - 9 comments

#46 - Xenium datasets coordinates

Issue - State: closed - Opened by flyfyyfyy 2 months ago - 5 comments

#45 - Image registration in Xenium dataset

Issue - State: closed - Opened by xiachenrui 3 months ago - 6 comments

#44 - BCNB dataset

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

#43 - Do we need to correct the batch effects of given datasets

Issue - State: open - Opened by HelloWorldLTY 3 months ago - 14 comments
Labels: scientific-discussion

#42 - Update README.md

Pull Request - State: closed - Opened by guillaumejaume 3 months ago

#41 - Add batch effect quantification methods

Pull Request - State: closed - Opened by pauldoucet 3 months ago

#41 - Add batch effect quantification methods

Pull Request - State: closed - Opened by pauldoucet 3 months ago

#40 - negative value in adata.obsm['spatial']

Issue - State: closed - Opened by xiachenrui 3 months ago - 2 comments

#39 - How large is the spot in Xenium data and ST data?

Issue - State: closed - Opened by kennethahah 3 months ago - 4 comments

#38 - Matching cell type annotations with AnnData gene expression vectors

Issue - State: closed - Opened by merelkuijs 3 months ago - 11 comments
Labels: enhancement

#37 - add patch coordinates when saving to .h5

Pull Request - State: closed - Opened by pauldoucet 3 months ago

#36 - 256 x 256 patches for each spot instead of 224 x 224?

Issue - State: closed - Opened by kennethahah 3 months ago - 4 comments

#35 - About cell type information

Issue - State: closed - Opened by nkuweili 3 months ago - 4 comments

#34 - Pre-processed data for the multimodal representation learning task

Issue - State: closed - Opened by hathawayxxh 3 months ago - 5 comments

#33 - cleanup bench + new foundation models

Pull Request - State: closed - Opened by pauldoucet 3 months ago

#32 - rm unused imports

Pull Request - State: closed - Opened by guillaumejaume 3 months ago

#31 - Import Error: ModuleNotFoundError for vision_transformer_latest

Issue - State: closed - Opened by oyjr 3 months ago - 4 comments

#30 - move core methods to hestcore

Pull Request - State: closed - Opened by pauldoucet 3 months ago

#29 - Wsi

Pull Request - State: closed - Opened by pauldoucet 3 months ago

#28 - TENX98 and TENX97 don't have pixel/array coordinates

Issue - State: closed - Opened by KalinNonchev 3 months ago - 2 comments

#27 - Why don't we use all the samples to construct the benchmark?

Issue - State: closed - Opened by huangtinglin 4 months ago - 2 comments
Labels: scientific-discussion

#26 - fix exception thrown if cucim installed

Pull Request - State: closed - Opened by pauldoucet 4 months ago

#25 - HEST-lib v1.1.0

Pull Request - State: closed - Opened by pauldoucet 4 months ago

#24 - Update HEST_v1_0_0 -> HEST_v1_0_2

Pull Request - State: closed - Opened by pauldoucet 4 months ago

#23 - add table with samples used in benchmark

Pull Request - State: closed - Opened by guillaumejaume 4 months ago

#22 - The inclusion relationship between HEST and HEST Benchmark.

Issue - State: closed - Opened by Hanminghao 4 months ago - 1 comment

#21 - Converting Hest data to Spatialdata

Issue - State: closed - Opened by SathiyaNManivannan 4 months ago - 1 comment
Labels: bug

#20 - Update README.md

Pull Request - State: closed - Opened by guillaumejaume 4 months ago

#19 - add pip install datasets instruction

Pull Request - State: closed - Opened by pauldoucet 4 months ago

#18 - setup autoapprove for HF repository

Pull Request - State: closed - Opened by pauldoucet 4 months ago

#17 - Fix huggingface download counter

Pull Request - State: closed - Opened by pauldoucet 4 months ago

#16 - high variance genes

Issue - State: open - Opened by jinxixiang 4 months ago - 2 comments
Labels: scientific-discussion

#15 - Normalize adata (found only log1p)

Issue - State: closed - Opened by rushin682 5 months ago - 3 comments
Labels: scientific-discussion

#14 - fix bench gene panel

Pull Request - State: closed - Opened by pauldoucet 5 months ago

#13 - low Pearson correlation for COAD, READ, HCC

Issue - State: open - Opened by NBitBuilder 5 months ago - 8 comments
Labels: scientific-discussion

#12 - Issue downloading datasets

Issue - State: closed - Opened by BioinfoTongLI 5 months ago - 2 comments

#11 - Improve load_hest

Pull Request - State: closed - Opened by pauldoucet 5 months ago

#10 - Update README.md

Pull Request - State: closed - Opened by pauldoucet 5 months ago

#9 - add total size of dataset

Pull Request - State: closed - Opened by pauldoucet 5 months ago

#8 - add adata description tutorial

Pull Request - State: closed - Opened by pauldoucet 5 months ago

#7 - clear output

Pull Request - State: closed - Opened by guillaumejaume 5 months ago

#6 - License

Pull Request - State: closed - Opened by guillaumejaume 5 months ago

#5 - Update README.md

Pull Request - State: closed - Opened by guillaumejaume 5 months ago

#4 - Add tutorials, make dataset public, resolve bugs

Pull Request - State: closed - Opened by pauldoucet 5 months ago

#3 - prepare for 1.0.0 release

Pull Request - State: closed - Opened by pauldoucet 5 months ago

#2 - Update README.md

Pull Request - State: closed - Opened by guillaumejaume 5 months ago

#1 - Prepare for release

Pull Request - State: closed - Opened by pauldoucet 5 months ago