greenelab/generic-expression-patterns issues and pull requests

#125 - Edit figures for GBP final proof

Pull Request - State: closed - Opened by ajlee21 almost 2 years ago - 2 comments

#124 - Minor figure format edits

Pull Request - State: closed - Opened by ajlee21 about 2 years ago - 1 comment

#123 - Add stats test based on reviewer comment

Pull Request - State: closed - Opened by ajlee21 about 2 years ago - 1 comment

#122 - Reorder figures based on mention in text

Pull Request - State: closed - Opened by ajlee21 over 2 years ago - 1 comment

#121 - Edit reviewer experiment

Pull Request - State: closed - Opened by ajlee21 over 2 years ago - 1 comment

#121 - Edit reviewer experiment

Pull Request - State: closed - Opened by ajlee21 over 2 years ago - 1 comment

#120 - Update readme

Pull Request - State: closed - Opened by ajlee21 over 2 years ago - 1 comment

#120 - Update readme

Pull Request - State: closed - Opened by ajlee21 over 2 years ago - 1 comment

#119 - Reviewer edits

Pull Request - State: closed - Opened by ajlee21 over 2 years ago - 3 comments

#119 - Reviewer edits

Pull Request - State: closed - Opened by ajlee21 over 2 years ago - 3 comments

#118 - DESeq2 warning about metadata variables that are integers

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

#117 - new_model_experiment/2_identify_common_and_specific_genes.ipynb produces KeyError: 'the label [pao1_hogan_metals] is not in the [index]'

Issue - State: closed - Opened by taylorreiter over 2 years ago - 9 comments

#116 - recommendations for a jumpy loss curve on the validation data set

Issue - State: closed - Opened by taylorreiter over 2 years ago - 7 comments

#115 - the notebook `1_process_and_train_vae.ipynb` unecessarily contains code to create a raw template experiment

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

#114 - config config_new_model_experiment.tsv is missing many required params

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

#113 - user needs to create output directory for `process.normalize_compendium`

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

#113 - user needs to create output directory for `process.normalize_compendium`

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

#112 - error with `utils.read_config`: SyntaxError: invalid syntax

Issue - State: closed - Opened by taylorreiter over 2 years ago - 6 comments

#112 - error with `utils.read_config`: SyntaxError: invalid syntax

Issue - State: closed - Opened by taylorreiter over 2 years ago - 6 comments

#111 - required granularity for `experiment_to_sample_filename` when building a new model

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

#110 - clarifying config file parameter meanings

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

#110 - clarifying config file parameter meanings

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

#109 - Advice for determining a good size for latent dimensions for a new model experiment

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

#108 - Config file/documentation discrepancy for `processed_compendium_filename`

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

#108 - Config file/documentation discrepancy for `processed_compendium_filename`

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

#107 - Question for new model experiment: are count data in the compendium raw or normalized?

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

#106 - unclear input requirement for new models: `scaler_filename`

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

#105 - recommendations for running sophie on new models

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

#105 - recommendations for running sophie on new models

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

#104 - unclear input file requirement for new models: `vae_model_dir`

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

#104 - unclear input file requirement for new models: `vae_model_dir`

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

#103 - Minor updates to figures

Pull Request - State: closed - Opened by ajlee21 almost 3 years ago

#103 - Minor updates to figures

Pull Request - State: closed - Opened by ajlee21 almost 3 years ago

#102 - Add a couple of small analysis based on reviewer comments

Pull Request - State: closed - Opened by ajlee21 almost 3 years ago

#102 - Add a couple of small analysis based on reviewer comments

Pull Request - State: closed - Opened by ajlee21 almost 3 years ago

#101 - Small refactor

Pull Request - State: closed - Opened by ajlee21 about 3 years ago

#101 - Small refactor

Pull Request - State: closed - Opened by ajlee21 about 3 years ago

#100 - Archive repository for manuscript

Issue - State: closed - Opened by ajlee21 about 3 years ago - 1 comment

#99 - Update comments in new_experiment and new_model_experiment

Issue - State: closed - Opened by ajlee21 about 3 years ago - 1 comment

#99 - Update comments in new_experiment and new_model_experiment

Issue - State: closed - Opened by ajlee21 about 3 years ago - 1 comment

#98 - Update to latest version of ponyo

Pull Request - State: closed - Opened by ajlee21 about 3 years ago

#98 - Update to latest version of ponyo

Pull Request - State: closed - Opened by ajlee21 about 3 years ago

#97 - Update analysis notebooks to use newest version of ponyo

Issue - State: closed - Opened by ajlee21 about 3 years ago - 1 comment

#97 - Update analysis notebooks to use newest version of ponyo

Issue - State: closed - Opened by ajlee21 about 3 years ago - 1 comment

#96 - Add new analysis using Pa rnaseq data

Pull Request - State: closed - Opened by ajlee21 about 3 years ago

#96 - Add new analysis using Pa rnaseq data

Pull Request - State: closed - Opened by ajlee21 about 3 years ago

#95 - Update Figure 5

Pull Request - State: closed - Opened by ajlee21 about 3 years ago

#95 - Update Figure 5

Pull Request - State: closed - Opened by ajlee21 about 3 years ago

#94 - Update workflow figure

Pull Request - State: closed - Opened by ajlee21 about 3 years ago - 1 comment

#94 - Update workflow figure

Pull Request - State: closed - Opened by ajlee21 about 3 years ago - 1 comment

#93 - Update readme with new crow et al analysis

Pull Request - State: closed - Opened by ajlee21 about 3 years ago

#93 - Update readme with new crow et al analysis

Pull Request - State: closed - Opened by ajlee21 about 3 years ago

#92 - Review Crow et al data and update figures

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#92 - Review Crow et al data and update figures

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#91 - Revise figures

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#91 - Revise figures

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#90 - Crow et al model

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 1 comment

#90 - Crow et al model

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 1 comment

#89 - Try MR normalized input data

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#89 - Try MR normalized input data

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#88 - How to modify config file for multiple analyses of the same dataset

Issue - State: closed - Opened by tessadgreen over 3 years ago - 5 comments

#88 - How to modify config file for multiple analyses of the same dataset

Issue - State: closed - Opened by tessadgreen over 3 years ago - 5 comments

#87 - Address user issues

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#87 - Address user issues

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#86 - Experiments to look into why common DEGs are found frequently

Issue - State: open - Opened by ajlee21 over 3 years ago

#86 - Experiments to look into why common DEGs are found frequently

Issue - State: open - Opened by ajlee21 over 3 years ago

#85 - Compare common vs other gene expression

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 3 comments

#85 - Compare common vs other gene expression

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 3 comments

#84 - Comments provided by Tessa (first SOPHIE user)

Issue - State: closed - Opened by ajlee21 over 3 years ago - 1 comment

#84 - Comments provided by Tessa (first SOPHIE user)

Issue - State: closed - Opened by ajlee21 over 3 years ago - 1 comment

#83 - Add sklearn version

Issue - State: closed - Opened by ajlee21 over 3 years ago - 1 comment

#83 - Add sklearn version

Issue - State: closed - Opened by ajlee21 over 3 years ago - 1 comment

#82 - Clarify documentation

Issue - State: closed - Opened by ajlee21 over 3 years ago - 2 comments

#82 - Clarify documentation

Issue - State: closed - Opened by ajlee21 over 3 years ago - 2 comments

#81 - More figure updates

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#81 - More figure updates

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#80 - Update figures with new acronym

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#80 - Update figures with new acronym

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#79 - Debug pytest failing

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 2 comments

#79 - Debug pytest failing

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 2 comments

#78 - Compare VAE vs noise simulation

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 3 comments

#78 - Compare VAE vs noise simulation

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 3 comments

#77 - Update manuscript figures

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#77 - Update manuscript figures

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#76 - RNA-seq only generic genes

Issue - State: open - Opened by ajlee21 over 3 years ago - 1 comment

#76 - RNA-seq only generic genes

Issue - State: open - Opened by ajlee21 over 3 years ago - 1 comment

#75 - More experiments looking into missing generic genes

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 1 comment

#75 - More experiments looking into missing generic genes

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 1 comment

#74 - Refactor repo

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#74 - Refactor repo

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#73 - Add new experiment examining counts before and after simulation

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#73 - Add new experiment examining counts before and after simulation

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#72 - Update manuscript figures

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#72 - Update manuscript figures

Pull Request - State: closed - Opened by ajlee21 over 3 years ago

#71 - Explore uncorrelated generic genes

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 2 comments

#71 - Explore uncorrelated generic genes

Pull Request - State: closed - Opened by ajlee21 over 3 years ago - 2 comments

#70 - Compare degree + centrality measures for generic vs. non-generic genes

Pull Request - State: closed - Opened by jjc2718 over 3 years ago - 2 comments

#70 - Compare degree + centrality measures for generic vs. non-generic genes

Pull Request - State: closed - Opened by jjc2718 over 3 years ago - 2 comments

#69 - Pytest failing

Issue - State: closed - Opened by ajlee21 over 3 years ago - 1 comment

#69 - Pytest failing

Issue - State: closed - Opened by ajlee21 over 3 years ago - 1 comment

GitHub / greenelab/generic-expression-patterns issues and pull requests