Ecosyste.ms: Issues

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GitHub / biofam/MOFA2 issues and pull requests

#166 - Update create_mofa.R

Pull Request - State: open - Opened by willisbillis about 1 month ago

#165 - Empty factors - Spatial Transcripomics data

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

#163 - not using the GPU well

Issue - State: open - Opened by dorothyzh 4 months ago

#163 - not using the GPU well

Issue - State: open - Opened by dorothyzh 4 months ago

#162 - prepare_mofa function doesn't seem to train the model

Issue - State: open - Opened by nis2034 4 months ago - 2 comments

#158 - plot_enrichment_detailed function is not creating labeled plots

Issue - State: open - Opened by velenjak1 6 months ago - 3 comments

#157 - Outdated links to tutorials on website

Issue - State: open - Opened by artur-sannikov 6 months ago - 1 comment

#156 - AttributeError: Module 'scipy' has no attribute 'shape'

Issue - State: open - Opened by nbutyrate 6 months ago - 7 comments

#154 - AttributeError: Module 'scipy' has no attribute 'shape'

Issue - State: open - Opened by madp4rry 7 months ago - 2 comments

#153 - AttributeError: Module 'scipy' has no attribute 'shape'

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

#151 - `get_factors` and `get_variance_explained`

Issue - State: open - Opened by artur-sannikov 7 months ago

#150 - Incorrect description of `plot_top_weights`?

Issue - State: open - Opened by artur-sannikov 7 months ago

#149 - Error in training options

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

#148 - Incorrect links to documentation on website

Issue - State: open - Opened by artur-sannikov 7 months ago

#146 - AttributeError: 'BayesNet' object has no attribute 'train_stats'

Issue - State: open - Opened by Marwansha 8 months ago - 2 comments

#145 - Get noise terms with MOFA2 R package

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

#144 - Implement mofa2 wrapper for MAE

Pull Request - State: open - Opened by RiboRings 9 months ago - 17 comments

#143 - geneID in place of Features

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

#142 - installation of package ‘basilisk’ had non-zero exit status

Issue - State: open - Opened by AlbertSL98 10 months ago - 1 comment

#140 - Fix .set colorby

Pull Request - State: closed - Opened by salix-d 10 months ago

#139 - Fix to .set_colorby

Pull Request - State: closed - Opened by salix-d 10 months ago

#138 - MOFA latent factors as predictor variables

Issue - State: open - Opened by zroger49 10 months ago

#137 - MOFAcell documentation

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

#136 - names(MOFAobject@expectations) keeps showing NULL

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

#135 - Prepare for upcoming Seurat v5 release

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

#134 - create_mofa_from_df issue

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

#133 - Extended support for MultiAssayExperiment

Issue - State: open - Opened by RiboRings about 1 year ago - 7 comments

#132 - Unsure whether to use groups

Issue - State: open - Opened by GabriellaS-K about 1 year ago

#131 - run_mofa stuck on iteration 49. optimising sigma node

Issue - State: closed - Opened by GabriellaS-K about 1 year ago - 5 comments

#130 - Dockerfile using R 4.3 or higher

Issue - State: open - Opened by casper937 about 1 year ago

#128 - Way to save model directly in R

Issue - State: open - Opened by hsiaoyi0504 over 1 year ago - 1 comment

#127 - Error with spikeslab_factors = TRUE

Issue - State: open - Opened by lujunyan1118 over 1 year ago - 2 comments

#126 - Handling view of categorical data of which levels > 2

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

#125 - Strategies using MOFA for integrating proteomic and CyTOF data

Issue - State: open - Opened by pdimitron over 1 year ago - 1 comment

#124 - `MOFAobject@expectations` is empty list

Issue - State: open - Opened by danli349 over 1 year ago - 1 comment

#122 - Found conflicts with python and glibc? please help

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

#121 - weird output after trained the mofa model

Issue - State: closed - Opened by ryf0810 over 1 year ago

#119 - AttributeError: Module 'scipy' has no attribute 'random'

Issue - State: open - Opened by ahucke over 1 year ago - 5 comments

#118 - Have samples that are missing some data modality

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

#117 - calculate_contribution_scores

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

#116 - Corrected link to template script in R.

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

#115 - model_opts$spikeslab_weights <- TRUE

Issue - State: open - Opened by ChristianRohde over 1 year ago - 3 comments

#114 - Issues running MOFA2 with Basilisk on Ubuntu <=18

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

#113 - Number of inducing points in MEFISTO

Issue - State: open - Opened by ttgump over 1 year ago - 1 comment

#112 - Problem on the python environment when run run_mofa

Issue - State: open - Opened by xinhuiwang almost 2 years ago - 1 comment

#110 - Projecting unseen (test) data to the trained latent space

Issue - State: open - Opened by borauyar almost 2 years ago - 1 comment

#109 - Update prepare_mofa.R

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

#107 - batch effcts and data integration

Issue - State: closed - Opened by wangjiawen2013 almost 2 years ago - 1 comment

#106 - How to deal with unbalanced number of replicates between views - MEFISTO

Issue - State: open - Opened by Eirinits almost 2 years ago - 1 comment

#105 - plot_factors: fix continuous color scale when plotting >2 factors

Pull Request - State: open - Opened by ilia-kats about 2 years ago

#104 - Implement GPU device selection (#103)

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

#103 - How to specify GPU device in MOFA2

Issue - State: open - Opened by yulijia about 2 years ago - 5 comments

#101 - Proper normalization for Proteomics and RNA-seq data

Issue - State: open - Opened by MonicaSteffi about 2 years ago - 2 comments

#100 - Can MOFA integrate different omics data from independent studies?

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

#99 - Error in get_expectations(object, "Z", as.data.frame) :

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

#98 - `Installation paths not writeable, unable to update packages`

Issue - State: open - Opened by bschilder about 2 years ago - 6 comments

#97 - Inconsistent scaling of feature weights in get_weights()

Issue - State: open - Opened by oliviaAB about 2 years ago

#95 - Add GPU/CUDA support in Docker image

Issue - State: open - Opened by frederikziebell about 2 years ago

#93 - total explained variance is larger than 100

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

#92 - How do I calculate one explained-variance value for each factor?

Issue - State: open - Opened by ravipatel4 over 2 years ago - 2 comments

#91 - Truncation of very long features names can lose uniqueness

Issue - State: open - Opened by frederikziebell over 2 years ago - 2 comments

#90 - Error in run_enrichment. feature.sets has to be a list or a binary matrix.

Issue - State: open - Opened by jiangfuqing over 2 years ago - 1 comment

#89 - matrix.please function not found

Issue - State: open - Opened by jiangfuqing over 2 years ago - 3 comments

#88 - create_mofa issue with different number of samples in different data types

Issue - State: open - Opened by clersdom over 2 years ago - 1 comment

#87 - Using multiple metadata as groups?

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

#85 - A problem with MEFISTO

Issue - State: closed - Opened by amitfrish over 2 years ago

#83 - Problems with legend of plot_factors()

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

#82 - Error in run_enrichment

Issue - State: closed - Opened by ProphetDarkland almost 3 years ago - 7 comments

#81 - Error in 'get_data' due to "matrix_placeholder" object

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

#80 - Question regarding correlate_factors_with_covariates

Issue - State: closed - Opened by FloraMika almost 3 years ago - 4 comments

#79 - Mofapy2 v0.6.4 won't run in R

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

#77 - fix url formatting

Pull Request - State: closed - Opened by jan-glx about 3 years ago

#76 - problem with mofa2 training

Issue - State: closed - Opened by gittina about 3 years ago - 9 comments

#75 - Improve error message when feature names are duplicated

Issue - State: closed - Opened by gtca about 3 years ago - 6 comments

#74 - Problem with load_model in R environment

Issue - State: closed - Opened by vinayduggi about 3 years ago - 6 comments

#73 - Problems with NA values

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

#72 - Problems creating MOFA object

Issue - State: closed - Opened by geraldocantelli about 3 years ago - 13 comments

#71 - doi no space

Pull Request - State: closed - Opened by alanocallaghan over 3 years ago - 3 comments

#70 - Version bump confuses reticulate

Issue - State: closed - Opened by emdann over 3 years ago - 1 comment