Ecosyste.ms: Issues

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GitHub / cbg-ethz/dce issues and pull requests

#37 - How can I change the number of nodes when plotting?

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

#36 - using TCGAsplitAssays instead of deprecated splitAssays (BioC error)

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

#35 - removed unused argument (na.value = 0.2)

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

#34 - Add qqconf dependency

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

#33 - bioc

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

#32 - added arbitrary distributions for simulated data #25

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

#31 - Update GTEx analysis to use TPM data

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

#30 - added GTEx validation

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

#29 - update latent simulation + citation

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

#28 - Fix mysterious `Error: subscript out of bounds` crash

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

#27 - added CARNIVAL + differential gene expression and readded LDGM

Pull Request - State: closed - Opened by MartinFXP over 3 years ago - 8 comments
Labels: enhancement

#26 - Deconfounding fix for real datasets

Pull Request - State: closed - Opened by dcevid almost 4 years ago - 1 comment

#25 - Feature: add arbitrary distribution choice to simulate data

Issue - State: closed - Opened by MartinFXP about 4 years ago - 2 comments
Labels: enhancement

#24 - bug in generating graph?

Issue - State: closed - Opened by dcevid about 4 years ago - 5 comments

#23 - Random DAG creation

Issue - State: closed - Opened by kpj over 4 years ago

#22 - Merge pathway nodes

Issue - State: closed - Opened by kpj over 4 years ago - 1 comment

#21 - TPM vs raw counts

Issue - State: closed - Opened by MartinFXP over 4 years ago - 1 comment

#20 - Open issues:

Issue - State: closed - Opened by MartinFXP almost 5 years ago - 3 comments

#19 - List of relevant pathway enrichment tools

Issue - State: closed - Opened by kpj almost 5 years ago - 6 comments

#18 - How to control the noise in (large) graphs?

Issue - State: closed - Opened by MartinFXP almost 5 years ago - 1 comment

#17 - How to benchmark perturbed ground truth?

Issue - State: closed - Opened by MartinFXP almost 5 years ago - 1 comment

#16 - Real pathways are incomplete

Issue - State: closed - Opened by kpj almost 5 years ago - 1 comment

#15 - How to validate (real data) biological results?

Issue - State: closed - Opened by kpj almost 5 years ago - 2 comments

#14 - Compare multiple performance measurements in benchmarking

Issue - State: closed - Opened by kpj almost 5 years ago - 1 comment

#13 - Input DAGs may not satisfy faithfulness assumption

Issue - State: closed - Opened by kpj about 5 years ago - 1 comment

#12 - How to choose the "correct" link function?

Issue - State: closed - Opened by kpj about 5 years ago - 4 comments

#11 - Simulating negative binomial read counts on DAGs

Issue - State: closed - Opened by kpj about 5 years ago - 5 comments

#10 - Using causal effects as edge weights can be misleading

Issue - State: closed - Opened by kpj about 5 years ago - 3 comments
Labels: enhancement

#9 - How to include library size in the model?

Issue - State: closed - Opened by MartinFXP about 5 years ago - 6 comments
Labels: enhancement

#8 - `glm.nb` throws warnings and errors when data is naughty

Issue - State: closed - Opened by kpj about 5 years ago - 3 comments
Labels: bug

#7 - Helpful links

Issue - State: closed - Opened by kpj about 5 years ago - 1 comment

#5 - How to generate synthetic expression profiles

Issue - State: closed - Opened by kpj about 5 years ago - 1 comment

#4 - Real pathways are not always DAGs

Issue - State: closed - Opened by kpj about 5 years ago - 1 comment
Labels: bug, help wanted, wontfix

#4 - Real pathways are not always DAGs

Issue - State: closed - Opened by kpj about 5 years ago - 1 comment
Labels: bug, help wanted, wontfix

#3 - Understand KEGG pathway structure

Issue - State: closed - Opened by kpj about 5 years ago - 1 comment

#2 - How to test for enrichment of a pathway?

Issue - State: closed - Opened by MartinFXP about 5 years ago - 4 comments
Labels: enhancement

#1 - How to proceed, if samples in tissue < genes in pathway?

Issue - State: closed - Opened by MartinFXP about 5 years ago - 3 comments