Ecosyste.ms: Issues

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

GitHub / snap-stanford/GEARS issues and pull requests

#90 - Compatibility issue with SciPy 1.15.1

Issue - State: closed - Opened by li-cris 9 days ago - 1 comment

#89 - Missing files for reproducing Fig 3c

Issue - State: open - Opened by chinaliye 3 months ago

#88 - uncertainty score question

Issue - State: closed - Opened by ernesto-iacucci 4 months ago - 2 comments

#87 - Interpreting the results of GI_predict()

Issue - State: closed - Opened by ManuelMoradiellos 4 months ago - 2 comments

#86 - Question about loss function of direction

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

#85 - test

Issue - State: closed - Opened by oscarpitcho 4 months ago

#83 - How is the adamson data generated?

Issue - State: closed - Opened by YOU-k 5 months ago - 1 comment

#82 - Question about mean baseline

Issue - State: open - Opened by Leafaeolian 5 months ago

#81 - KeyError 'val' when creating dataloader with split='single'

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

#80 - Pretrained Reploge2022 model

Issue - State: open - Opened by Jiahao-Gao 6 months ago

#79 - Questions about creating pertdata with own data files

Issue - State: open - Opened by HelloWorldLTY 7 months ago - 3 comments

#77 - Question about "Using Trained Model"

Issue - State: closed - Opened by incase-1 7 months ago - 1 comment

#76 - Unpickling Error in gene_set_path

Issue - State: open - Opened by bioinfonewguy 7 months ago - 3 comments

#75 - Value error in loading the dataset

Issue - State: closed - Opened by bboyrush117 7 months ago - 2 comments

#74 - Beginner question: GEARS on un-perturbed data

Issue - State: closed - Opened by bioinfonewguy 8 months ago - 1 comment

#71 - KeyError: 'val'

Issue - State: closed - Opened by xiaomaolxc 8 months ago - 4 comments

#70 - Environments (versions of packages) to run GEARS

Issue - State: open - Opened by wcanisay-y 9 months ago

#69 - Mixup in hyperparameters for H_pert H_gene?

Issue - State: open - Opened by mhorlacher 9 months ago

#68 - Duplicated gene names in replogle_k562_essential

Issue - State: closed - Opened by zhan8855 9 months ago - 4 comments

#67 - Are there pretrained weights available?

Issue - State: closed - Opened by jamesbraza 10 months ago - 1 comment

#66 - Moving `torch.device` to work in Google Colab

Issue - State: closed - Opened by jamesbraza 10 months ago - 1 comment

#65 - Missing `torch_geometric` in `requirements.txt`

Issue - State: closed - Opened by jamesbraza 10 months ago - 1 comment

#64 - error about prepare_split

Issue - State: closed - Opened by oahux28 10 months ago - 4 comments

#63 - Question about how to generate condition colname?

Issue - State: closed - Opened by yanwuanxin 10 months ago - 3 comments

#62 - Custom PertData ``new_data_process`` error

Issue - State: open - Opened by Yonggie 10 months ago - 1 comment

#61 - differences between papers and implementations

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

#60 - custom GO graph location

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

#58 - Questions about reproduction of Figure2f and Figure2cd

Issue - State: open - Opened by yu3jun 11 months ago - 1 comment

#57 - How to obtain more top_non_dropout_de?

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

#56 - KeyError: 'val'

Issue - State: closed - Opened by yanwuanxin 11 months ago - 5 comments

#55 - Questions about split and the experiment results

Issue - State: closed - Opened by Elvis-tan 11 months ago

#54 - Perturbations are not in the GO graph

Issue - State: closed - Opened by niklasbinder 12 months ago - 4 comments

#53 - Directly implementing gears on scRNA-seq data

Issue - State: closed - Opened by XiaoMi93 12 months ago - 3 comments

#52 - A question about directional loss.

Issue - State: closed - Opened by Bunnybeibei 12 months ago - 1 comment

#51 - Questions about reproduction of Figure2cd

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

#50 - Publication of model parameters

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

#49 - Trouble using the outputs obtained from the GEARS model

Issue - State: closed - Opened by fratajcz 12 months ago - 5 comments

#48 - perturbation coexpression

Issue - State: closed - Opened by xinghao-1210 about 1 year ago - 1 comment

#47 - Interpretation of Prediction

Issue - State: closed - Opened by uddamvathanak about 1 year ago - 4 comments

#46 - prediction interpretation

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

#45 - Issue with new_data_process function

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

#44 - tutorial_inference_Norman.ipynb is out-of-date

Issue - State: open - Opened by jzqin about 1 year ago - 5 comments

#43 - How to define pertubation?

Issue - State: closed - Opened by Larrycpan about 1 year ago - 2 comments

#42 - MLP module last layer activation is always set to ReLU

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

#41 - Matching to Different Set of Controls

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

#40 - About the preparation of split

Issue - State: closed - Opened by GoldenRain-Su about 1 year ago - 4 comments

#39 - Issue loading custom data

Issue - State: closed - Opened by docmab23 about 1 year ago - 2 comments

#38 - No file in https://dataverse.harvard.edu/api/accsess/datafile/6934319

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

#36 - A question about the direction loss

Issue - State: closed - Opened by zhan8855 over 1 year ago - 3 comments

#35 - Any suggestions for the HPC requirement

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

#34 - Very long import time

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

#33 - traing stack using the v0.10.0 gears

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

#32 - Error when trying to load the pre-trained model

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

#29 - no_test option for data split yields error

Issue - State: closed - Opened by ekernf01 over 1 year ago - 6 comments

#28 - Question on data pre-processing

Issue - State: closed - Opened by cbirchsy over 1 year ago - 9 comments

#27 - A question about selecting genes

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

#26 - IndexError: index 0 is out of bounds for axis 0 with size 0

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

#25 - Questions on pert_data.prepare_split

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

#24 - Bug in new_data_process

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

#23 - Please give some suggestions for fly scRNA-seq analysis?

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

#22 - problems with dataloader between versions

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

#21 - Refactor

Pull Request - State: closed - Opened by yhr91 over 1 year ago

#20 - ValueError: must produce aggregated value

Issue - State: closed - Opened by ekernf01 over 1 year ago - 2 comments

#19 - Train/Test GEARS on One Gene Perturbation

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

#18 - Problem in loading a subset of Dixit dataset

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

#17 - Add support for perturbation magnitude/direction

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

#16 - split questions

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

#15 - Fix error message for bad input in GEARS.predict()

Pull Request - State: closed - Opened by ekernf01 almost 2 years ago - 1 comment

#14 - Minimal example of data loading fails

Issue - State: closed - Opened by ekernf01 almost 2 years ago - 4 comments

#13 - Inference of a new gene

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

#12 - Support for combinations of gene activation and repression

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

#11 - More than 2 perturbations per cell in training data

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

#10 - Question: GO-network(s) with hierarchy separation?

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

#8 - Question about installation

Issue - State: closed - Opened by abedkurdi about 2 years ago - 1 comment

#7 - Questions about the implementation

Issue - State: closed - Opened by chocolate9624 over 2 years ago - 1 comment

#6 - A question about the condition columns in adata.obs

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

#5 - Reproduce figure 2 b-g

Issue - State: closed - Opened by subercui over 2 years ago - 23 comments

#4 - Demo notebook raises gradient error for torch 1.12

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

#3 - black formatting

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

#2 - Install instructions

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

#1 - Create LICENSE

Pull Request - State: closed - Opened by kexinhuang12345 over 2 years ago