Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / biofam/MOFA2 issues and pull requests
#168 - incorrect plot margins in correlate_factors_with_covariates
Issue -
State: open - Opened by Cleiti 14 days ago
#167 - Questions about using MOFA with bulk RNA-seq deconvolution results and uneven view sizes
Issue -
State: open - Opened by doctorfaraday520 18 days ago
#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
#164 - run_enrichment does not work when selecting a single factor
Issue -
State: open - Opened by jjcaff 4 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
#161 - The `<scale>` argument of `guides()` cannot be `FALSE` deprecation
Issue -
State: open - Opened by artur-sannikov 5 months ago
#160 - Error: run_enrichment error feature.sets has to be a list or a binary matrix.**
Issue -
State: open - Opened by mluciarr 5 months ago
#159 - Error: Error in h5checktype(). H5Identifier not valid.
Issue -
State: open - Opened by mluciarr 6 months ago
#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#157 - Outdated links to tutorials on website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
#155 - Error in create_mofa_from_Seurat(BJ, groups = NULL, assays = c("RNA", :
Issue -
State: open - Opened by nbutyrate 6 months ago
#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
#152 - `correlate_covariates`: redundant conversion to numeric and incorrect warning
Issue -
State: open - Opened by artur-sannikov 7 months ago
- 1 comment
#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
#147 - Mefisto error - ValueError: operands could not be broadcast together with shapes (10,1) (23,1)
Issue -
State: open - Opened by saum-kmr 8 months ago
- 5 comments
#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
#141 - Bugs with the argument color_by and shape_by in plot_weights
Issue -
State: open - Opened by salix-d 10 months ago
#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
#129 - Why weights need to be interpreted as relative value to 1 instead of absolute scale
Issue -
State: open - Opened by gmhhope 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
#123 - Can I analyze bulk RNAseq and bulk ATACseq together using `MOFA2`?
Issue -
State: open - Opened by danli349 over 1 year ago
#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
#120 - Rcmd configure.win impaired when R_HOME path contains space
Issue -
State: open - Opened by liuhuoz 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$spikeslab_weights <- TRUE
Issue -
State: open - Opened by ChristianRohde over 1 year ago
- 3 comments
#114 - Issues running MOFA2 with Basilisk on Ubuntu <=18
Issue -
State: open - Opened by dpmerrell over 1 year ago
#113 - Number of inducing points in MEFISTO
Issue -
State: open - Opened by ttgump over 1 year ago
- 1 comment
#112 - Problem on the python environment when run run_mofa
Issue -
State: open - Opened by xinhuiwang almost 2 years ago
- 1 comment
#111 - Bioconductor 3.16's MOFA2 refers to no-longer-existing function basilisk.utils::installMiniconda
Issue -
State: open - Opened by github-rena almost 2 years ago
#110 - Projecting unseen (test) data to the trained latent space
Issue -
State: open - Opened by borauyar almost 2 years ago
- 1 comment
#109 - Update prepare_mofa.R
Pull Request -
State: closed - Opened by frederikziebell almost 2 years ago
- 2 comments
#108 - Error in py_call_impl(callable, dots$args, dots$keywords): AttributeError: Module 'scipy' has no attribute 'random'
Issue -
State: open - Opened by royfrancis almost 2 years ago
- 8 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
#102 - Problem with adding Feature metadata in Single Cell Multiome RNA+ATAC Tutorial
Issue -
State: open - Opened by jblich870 about 2 years ago
#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
#96 - MEFISTO error with plot_interpolation_vs_covariate() when some factors have been removed
Issue -
State: closed - Opened by oliviaAB about 2 years ago
- 3 comments
#95 - Add GPU/CUDA support in Docker image
Issue -
State: open - Opened by frederikziebell about 2 years ago
#94 - Improve documentation for argument factors in plot_factors()
Issue -
State: open - Opened by frederikziebell over 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
#86 - Issue with factor exploration: "NA/NaN/Inf in foreign function call (arg 10)"
Issue -
State: open - Opened by jasiozaucha over 2 years ago
#85 - A problem with MEFISTO
Issue -
State: closed - Opened by amitfrish over 2 years ago
#84 - Error with long feature_names strings, duplicated feature_names
Issue -
State: closed - Opened by jmirobla 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
#78 - plot_data_overview and loading model from hdf5 always indicate wrong number of features per view and number of samples per group
Issue -
State: closed - Opened by marangiop about 3 years ago
- 1 comment
#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