Ecosyste.ms: Issues

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

GitHub / YosefLab/mrvi issues and pull requests

#105 - Reproducibility issue of MRVI

Issue - State: open - Opened by Nusob888 7 months ago

#104 - Loading saved model fails

Issue - State: open - Opened by VladimirShitov 8 months ago - 3 comments

#103 - Add deprecation warnings for 1.0.1

Pull Request - State: closed - Opened by justjhong 9 months ago

#102 - Remove pd.Series accession warnings

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

#101 - Rm statsmodels dep

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

#100 - Bug fix for compute_local_sample_distances

Pull Request - State: closed - Opened by justjhong 10 months ago - 1 comment
Labels: cuda tests

#99 - Fix de/da bug for non ordered int sample keys

Pull Request - State: closed - Opened by justjhong 10 months ago
Labels: cuda tests

#98 - DE/DA method refactor

Pull Request - State: closed - Opened by justjhong 11 months ago - 1 comment
Labels: cuda tests

#96 - Produce user-guide and tutorial

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

#95 - Reformat and simplify DA pipeline

Issue - State: closed - Opened by PierreBoyeau 11 months ago

#94 - Rename DE module

Issue - State: closed - Opened by PierreBoyeau 11 months ago

#93 - [ci] remove prereleases flag from tests

Pull Request - State: closed - Opened by martinkim0 12 months ago

#92 - Normalization does not clip distances at 0

Pull Request - State: closed - Opened by justjhong 12 months ago - 1 comment
Labels: cuda tests

#91 - z_u_prior false should remove the prior

Pull Request - State: closed - Opened by justjhong 12 months ago - 1 comment
Labels: cuda tests

#90 - minimal user guide

Pull Request - State: closed - Opened by PierreBoyeau 12 months ago

#89 - Prepare for v1.0.0b1

Pull Request - State: closed - Opened by justjhong 12 months ago
Labels: cuda tests

#88 - Rm deprecated

Pull Request - State: closed - Opened by PierreBoyeau 12 months ago

#87 - Add back sparse and xarray deps, lower bound scvi-tools

Pull Request - State: closed - Opened by martinkim0 12 months ago

#86 - Add install from scvi-tools main to workflows

Pull Request - State: closed - Opened by martinkim0 12 months ago

#84 - Reduce mem footprint of `get_latent_representation`

Pull Request - State: closed - Opened by martinkim0 about 1 year ago - 2 comments
Labels: all tests

#83 - Rename scvi-v2 to mrvi

Pull Request - State: closed - Opened by martinkim0 about 1 year ago

#81 - Release checklist for preprint tag

Issue - State: closed - Opened by martinkim0 about 1 year ago

#80 - Increase lower bound on scvi-tools, remove deps

Pull Request - State: closed - Opened by martinkim0 about 1 year ago

#77 - ablation

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

#76 - Update _model.py

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

#73 - Extended sets

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

#72 - WIP implement decoding

Pull Request - State: closed - Opened by Dana2670 over 1 year ago - 1 comment

#68 - Add new "ball" flavor of admissibility function

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

#59 - stop gradients option in attention block

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

#58 - Attention from z to x

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

#52 - Adam regs

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

#48 - Select samples based on # of DEGs

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

#47 - New baselines

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

#46 - Amat prior

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

#44 - `IndexError` raised when computing local reps

Issue - State: closed - Opened by PierreBoyeau about 2 years ago

#39 - scalability issues

Issue - State: closed - Opened by PierreBoyeau about 2 years ago

#38 - [WIP] Rank most correlated genes / get DE genes with distance matrices

Pull Request - State: closed - Opened by PierreBoyeau about 2 years ago - 1 comment

#36 - Autocorr module

Issue - State: closed - Opened by PierreBoyeau about 2 years ago

#32 - hierarchy poc

Pull Request - State: closed - Opened by PierreBoyeau about 2 years ago - 1 comment

#27 - nonlinear u -> z encoder

Issue - State: closed - Opened by PierreBoyeau about 2 years ago

#25 - First try at deg pred

Pull Request - State: closed - Opened by PierreBoyeau about 2 years ago - 3 comments

#23 - High dimensional analysis

Issue - State: closed - Opened by adamgayoso about 2 years ago
Labels: experiments

#21 - Out of distribution masking of samples

Issue - State: closed - Opened by adamgayoso about 2 years ago
Labels: experiments

#20 - Taking counterfactual samples through to gex to rank genes

Issue - State: closed - Opened by adamgayoso about 2 years ago - 1 comment
Labels: experiments

#19 - 1000 donor PBMC dataset

Issue - State: closed - Opened by adamgayoso about 2 years ago - 1 comment
Labels: experiments

#18 - sciplex dataset

Issue - State: closed - Opened by adamgayoso about 2 years ago
Labels: experiments

#18 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: open - Opened by pre-commit-ci[bot] 12 months ago

#17 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago - 1 comment

#17 - Sample embedding

Issue - State: closed - Opened by adamgayoso about 2 years ago
Labels: architecture

#16 - scIB benchmarking

Issue - State: closed - Opened by adamgayoso about 2 years ago - 1 comment
Labels: experiments

#16 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] about 1 year ago - 1 comment

#15 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#14 - Experiment with downsampling one sample in one cell type

Issue - State: closed - Opened by adamgayoso about 2 years ago - 2 comments
Labels: experiments

#14 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] over 1 year ago - 1 comment

#13 - Rerelease 0.2.0 on PyPI

Issue - State: closed - Opened by martinkim0 over 1 year ago - 3 comments

#12 - Bump version to 0.2.0

Pull Request - State: closed - Opened by martinkim0 over 1 year ago

#11 - [WIP] Uncertainty POC for MrVI

Pull Request - State: closed - Opened by PierreBoyeau about 2 years ago - 1 comment

#11 - Update dependencies and code for scvi-tools >= 1.0.0

Pull Request - State: closed - Opened by martinkim0 over 1 year ago - 1 comment

#10 - Improving scalability for large datasets

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

#9 - Fix reproducibility with torch impl

Pull Request - State: closed - Opened by justjhong about 2 years ago - 1 comment

#9 - update LossRecorder to LossOutput

Pull Request - State: closed - Opened by rpeys over 1 year ago - 4 comments

#8 - Import fails with scvi-tools >= 0.20

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

#7 - [pre-commit.ci] pre-commit autoupdate

Pull Request - State: closed - Opened by pre-commit-ci[bot] almost 2 years ago - 2 comments

#6 - Update for scvi v0.20

Pull Request - State: closed - Opened by martinkim0 almost 2 years ago - 1 comment

#4 - Cleanup terminology and unused code

Pull Request - State: closed - Opened by justjhong over 2 years ago - 1 comment

#3 - Change metric to euclidean

Pull Request - State: closed - Opened by justjhong over 2 years ago - 1 comment

#2 - Add method to output pairwise distances

Pull Request - State: closed - Opened by justjhong over 2 years ago - 1 comment

#1 - Readme, update method names

Pull Request - State: closed - Opened by adamgayoso over 2 years ago - 1 comment