Ecosyste.ms: Issues

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GitHub / theislab/cpa issues and pull requests

#60 - About sciplex3 dataset in Figure 2

Issue - State: open - Opened by ranzhran 3 months ago - 1 comment

#58 - CPA environment issues

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

#56 - Pre-trained model for sciplex data?

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

#55 - fix register_fields bug in tuner and add dependencies

Pull Request - State: open - Opened by chelseabright96 5 months ago

#54 - Autotuner not saving results

Issue - State: open - Opened by pgm99 5 months ago - 1 comment

#52 - Batch correction in expression space data set unavailable

Issue - State: closed - Opened by fabi-lab 5 months ago - 1 comment

#51 - Incompatible packages make me unable to use CPA outside of Colab

Issue - State: closed - Opened by ZaneDash 5 months ago - 7 comments

#50 - Issue Installing CPA

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

#49 - How do I apply CPA to new control cells?

Issue - State: open - Opened by MUCDK 7 months ago

#48 - Tuner fix added #47

Pull Request - State: closed - Opened by ArianAmani 8 months ago

#47 - Tuner isn't logging plan_kwargs on WandB

Issue - State: closed - Opened by ArianAmani 8 months ago
Labels: bug

#46 - Arian amani/issue45

Pull Request - State: closed - Opened by ArianAmani 8 months ago
Labels: enhancement

#45 - HyperParameter Tuning Script

Issue - State: closed - Opened by ArianAmani 8 months ago
Labels: enhancement

#44 - The code is licensed for Yosef Lab

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

#43 - fix jax deps

Pull Request - State: closed - Opened by zgr2788 9 months ago - 1 comment

#42 - Generalization to unseen categories

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

#40 - Norman tutorial question

Issue - State: open - Opened by chujunhe 9 months ago - 1 comment

#38 - Prediction on unseen dataset without overlap

Issue - State: open - Opened by xinghao-1210 11 months ago

#37 - How to optmize CPA hyperparamters

Issue - State: closed - Opened by AxKo 12 months ago - 6 comments

#36 - Model Training Error

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

#35 - How to use external gene embedding in CPA?

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

#34 - Install CPA dependencies fixed

Pull Request - State: closed - Opened by ArianAmani about 1 year ago

#33 - Update review branch

Pull Request - State: closed - Opened by ArianAmani about 1 year ago

#32 - Understanding your tutorial using the Norman (2019) data ...

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

#31 - Changed dependency versions

Pull Request - State: closed - Opened by ArianAmani about 1 year ago

#30 - custom_predict more clean

Pull Request - State: closed - Opened by ArianAmani about 1 year ago

#29 - fixed jax version (new update)

Pull Request - State: closed - Opened by ArianAmani about 1 year ago

#28 - Added custom latent/expression reconstruction functionality.

Pull Request - State: closed - Opened by ArianAmani about 1 year ago

#27 - Predicting using trained model.

Issue - State: open - Opened by faith-8 about 1 year ago - 5 comments

#26 - Maintenance: Fixing bugs, typos, version conflicts, etc.

Pull Request - State: closed - Opened by ArianAmani about 1 year ago - 1 comment
Labels: bug, documentation, enhancement

#25 - installation.rst hyperlink typo fixed

Pull Request - State: closed - Opened by ArianAmani about 1 year ago

#23 - cpa.pl.plot_history does not include valid

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

#22 - model.predict() error: cannot unpack non-iterable NoneType object

Issue - State: open - Opened by znavidi about 1 year ago - 2 comments

#21 - dependencies: change python-igraph to igraph

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

#20 - v0.5 "ValueError: Expected a parent" in tutorial

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

#19 - Trained models

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

#18 - tutorial CPAModule.init

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

#17 - AttributeError: module 'cpa' has no attribute 'CPA'

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

#16 - Run CPA on Kang et al dataset without dosage information

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

#15 - Colab error when running setup_anndata()

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

#14 - Fix memory leak

Pull Request - State: closed - Opened by yanwu2014 over 1 year ago

#13 - updates need for scvi-tools 0.20

Issue - State: closed - Opened by cosnicolaou almost 2 years ago

#12 - updates for scvi-tools 0.20

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

#11 - TypeError: __init__() got an unexpected keyword argument 'checkpoint_callback'

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

#10 - Hyperparameter optimization

Issue - State: closed - Opened by yanwu2014 about 2 years ago - 2 comments

#9 - which version ? The theislab version or facebook version?

Issue - State: open - Opened by bitcometz over 2 years ago

#8 - Pre-processing for bulk RNA-seq?

Issue - State: open - Opened by bitcometz over 2 years ago

#7 - Errors in running notebook

Issue - State: closed - Opened by wershofe over 2 years ago - 5 comments

#6 - The versions for scvi-tools for CPA

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

#5 - Failed to run the notebook in colab

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

#4 - AttributeError: 'tuple' object has no attribute 'copy'

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

#3 - very different results from the notebook

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

#2 - ImportError due to torchmetrics

Issue - State: closed - Opened by mdmanurung over 2 years ago - 6 comments
Labels: enhancement

#1 - finish CPA implementation

Issue - State: closed - Opened by M0hammadL almost 3 years ago