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EngreitzLab
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gene_network_evaluation
Evaluation framework for computationally inferred gene networks from single-cell data.
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Ensure consistency of multiple test correction methods
#50
adamklie
opened
3 days ago
0
Get a demo dashboard for TeloHAEC on a server and shared
#49
adamklie
opened
4 days ago
0
Rerun Endothelial evaluation pipeline after update
#48
adamklie
opened
4 days ago
0
Add log2fc and FDR to association test outputs
#47
aron0093
closed
4 days ago
2
Fix: categorical association dataframe output
#46
aron0093
opened
5 days ago
3
Replace `pymemesuite` FIMO implementation with `tangermeme`
#45
adamklie
opened
1 week ago
0
Rerun iPSC_EC evaluation pipeline after update
#44
adamklie
opened
1 week ago
0
Add Topyic inference in `examples/inference/iPSC_EC/Topyfic`
#43
adamklie
opened
1 week ago
0
Add cNMF inference code to `examples/inference/iPSC_EC/cNMF`
#42
adamklie
opened
1 week ago
0
Code maintenance and good practices
#41
aron0093
opened
1 week ago
0
Update snakemake README to indicate its work in progress
#40
aron0093
opened
1 week ago
0
Jamboree gene programs 2024
#39
aron0093
closed
1 week ago
0
Merge back into dev
#38
aron0093
closed
1 week ago
0
Update README.md
#37
aron0093
closed
1 week ago
0
Add an evaluation for model robustness
#36
aron0093
opened
1 week ago
0
Jamboree gene programs 2024
#35
adamklie
closed
1 week ago
0
Expose motif match significance threshold to users for motif enrichment
#34
aron0093
opened
1 week ago
1
Add support for perturbation association tests stratified per categorical level
#33
aron0093
opened
1 week ago
2
Calibration of association tests
#32
aron0093
opened
1 week ago
0
General procedure to assess goodness of fit rather than explained variance ratio.
#31
aron0093
opened
1 week ago
0
Add Topyfic snakemake
#30
nargesr
closed
2 weeks ago
1
Update gene set enrichment functionality
#29
adamklie
opened
3 weeks ago
3
GSEA plot for individual program / term enrichment
#28
adamklie
opened
3 weeks ago
0
Align dashboard with config from evaluation pipeline
#27
adamklie
opened
3 weeks ago
0
Trait enrichment results should be processed in evaluations
#26
adamklie
opened
3 weeks ago
1
Single run analysis page, Section 2: Covariate association
#25
adamklie
closed
4 days ago
1
Structure plot
#24
adamklie
opened
3 weeks ago
0
Topic-trait correlation heatmap
#23
adamklie
closed
4 days ago
2
How do we define a term as uniquely enriched or associated?
#22
adamklie
closed
4 days ago
2
How are we handling promoter vs enhancer motif outputs from evaluation?
#21
adamklie
opened
3 weeks ago
4
Adding package versions to outputs from evaluation and (potentially) inference
#20
adamklie
opened
3 weeks ago
0
Should we deprecate all the GRN stuff for now?
#19
adamklie
opened
3 weeks ago
2
Update README to reflect current state of the evaluations offered
#18
adamklie
opened
3 weeks ago
0
Dashapp updates
#17
adamklie
closed
3 weeks ago
0
Bugfix: Changed program to program_name in test output for consistency.
#16
aron0093
closed
1 month ago
0
Rename column in `compute_perturbation_association` to "program_name" for consistency
#15
adamklie
closed
3 weeks ago
0
support for signficant program detection per guide-target and misc. bugfixes
#14
aron0093
closed
1 month ago
0
Preliminary dashapp
#13
adamklie
closed
2 months ago
0
Celloracle updates
#12
adamklie
closed
4 months ago
0
Dictys for GRN Models
#11
GaryCloudY
closed
4 months ago
0
Small -- Add Continuous Trait GWAS
#10
anderseng
closed
4 months ago
0
Add GWAS-based benchmarking pipeline & refactor geneset enrichment funs to output .csvs
#9
anderseng
closed
4 months ago
1
Adding plotting options and Topyfic workflow
#8
nargesr
closed
5 months ago
0
Query OpenTargets and GWAS Create Adjacency Matrix for GSEA
#7
anderseng
closed
5 months ago
1
scenic+ snakemake implementation
#6
adamklie
closed
6 months ago
0
Update README.md
#5
aron0093
closed
7 months ago
0
ported over code, env and rules from scenic+
#4
adamklie
closed
7 months ago
0
Minor updates on gene_enrichment.py to adjust for the data format as in mudata from factor analysis
#3
liusi2019
closed
7 months ago
1
add opoirion evaluation linkage
#2
opoirion
closed
7 months ago
1
Update README.md
#1
aron0093
closed
7 months ago
0
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