Lotfollahi-lab/nichecompass issues and pull requests

#75 - Gene program files

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

#74 - Problem creating NicheCompass model

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

#73 - Update package version and release notes

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

#72 - Revision

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

#71 - Kernel crashing when training the model with an adata (Visium HD) with 600k bins

Issue - State: closed - Opened by Rafael-Silva-Oliveira 6 months ago - 7 comments

#70 - _compute_connectivities_umap

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

#69 - Compatibility with Visium HD data (8 micron)

Issue - State: closed - Opened by Rafael-Silva-Oliveira 6 months ago - 4 comments

#68 - move scglue to optional dependency

Pull Request - State: closed - Opened by adamrboxall 7 months ago

#67 - installation requires pybedtools

Issue - State: closed - Opened by adamrboxall 7 months ago

#66 - MERFISH sample without GPs

Issue - State: closed - Opened by Dana162001 9 months ago - 9 comments

#65 - ValueError: max() arg is an empty sequence [Error during the model training]

Issue - State: closed - Opened by hkeremcil 9 months ago - 6 comments

#64 - Can I run NicheCompass with zebrafish Visium data?

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

#63 - Cannot replicate the result in the multimodal_tutorials

Issue - State: closed - Opened by dyxmvp 11 months ago - 3 comments

#62 - Tutorials review

Pull Request - State: closed - Opened by ArianAmani 11 months ago

#61 - Change data type of latent representation to improve scaling

Pull Request - State: closed - Opened by sebastianbirk 11 months ago

#60 - Status badges

Pull Request - State: closed - Opened by ArianAmani 11 months ago

#59 - clustering requires manual downstream processing, but is resource intensive

Issue - State: closed - Opened by adamrboxall 12 months ago

#58 - no way to export mu and std for active gps from the model conveniently

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

#57 - reference-query training cannot be performed with mismatched gene coverage

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

#56 - GP annotations files missing

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

#55 - add simple model evaluation

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

#54 - 50 add cli

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

#53 - deployment on HPC environments is difficult due to compatibility issues

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

#52 - Feature/communication network rework

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

#51 - reduce repo size

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

#50 - add CLI to wrap 'reproducibility' scripts

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

#49 - add minimal tests

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

#48 - refactor run configuration

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

#47 - 46 add devcontainer

Pull Request - State: closed - Opened by adamrboxall over 1 year ago - 3 comments

#46 - fix compatibility issues for development

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

#45 - CLean up gp summary retrieval

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

#44 - Backup/after addon redesign

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

#43 - Feature/decoder redesign

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

#42 - Bugfix/l1 mask

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

#41 - Feature/cat covariates

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

#40 - Feature/gp mask rework

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

#39 - Complete rebranding

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

#38 - Feature/atac analysis capabilities

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

#37 - Feature/atac seq multimodal model

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

#36 - Feature/atac seq multimodal model

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

#35 - Modify negative edge sampling to discard edges across conditions

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

#34 - Feature/cosine sim decoder

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

#33 - Feature/agg attention weight retrieval

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

#32 - Feature/denovo gps

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

#31 - Feature/query mapping

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

#30 - Feature/query mapping

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

#29 - Dev

Pull Request - State: closed - Opened by sebastianbirk about 2 years ago

#28 - Improvements in latent representation retrieval

Pull Request - State: closed - Opened by sebastianbirk about 2 years ago

#27 - Benchmarking of active gene programs

Pull Request - State: closed - Opened by sebastianbirk about 2 years ago

#26 - Add node-level mse computation

Pull Request - State: closed - Opened by sebastianbirk about 2 years ago

#25 - Add mebocost gps

Pull Request - State: closed - Opened by sebastianbirk about 2 years ago

#24 - Separate workflow into multiple notebooks

Pull Request - State: closed - Opened by sebastianbirk about 2 years ago

#23 - First version of autotalker for benchmarking

Pull Request - State: closed - Opened by sebastianbirk about 2 years ago

#22 - Major rework of autotalker model and VGPGAE neural net module (nb loss introduction, group lasso...)

Pull Request - State: closed - Opened by sebastianbirk about 2 years ago

#21 - Dev

Pull Request - State: closed - Opened by sebastianbirk about 2 years ago

#20 - Dev

Pull Request - State: closed - Opened by sebastianbirk about 2 years ago