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theislab
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mubind-benchmark
snakemake and notebook results for mubind package (weekly results )
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Time for pipeline as part of the final log
#35
ilibarra
opened
1 year ago
0
Merge probound-scrape to development
#34
ege-erdogan
closed
1 year ago
1
probound scraping/analysis notebook
#33
ege-erdogan
closed
1 year ago
2
Include in pipeline fits with sequence bias kernels i.e. 4x1 or 4x2 kernels, without extension.
#32
ilibarra
opened
1 year ago
0
Different optimizers
#31
ilibarra
opened
1 year ago
0
Probound scrape
#30
ege-erdogan
closed
1 year ago
1
Pairwise predictions with related proteins
#29
ilibarra
opened
1 year ago
0
comparison with motif deviations from chromvar
#28
ilibarra
opened
1 year ago
0
write/read read counts as sparse matrices
#27
ilibarra
closed
1 year ago
1
input/output by rule into directories with same name
#26
ilibarra
opened
1 year ago
0
automated way to test snakemake pipeline (similar to small pytest).
#25
ilibarra
closed
1 year ago
1
Comparison of learned/aggregated filters with CisBP, JASPAR, and/or Archetypes
#24
ilibarra
opened
1 year ago
0
Comparison of R2s between mubind and ProBound
#23
ilibarra
opened
1 year ago
2
record total counts per query
#22
ege-erdogan
closed
1 year ago
0
refine_models step
#21
ilibarra
opened
1 year ago
1
rule reduce_filters_dataset after fit_model.py
#20
ilibarra
opened
1 year ago
0
Modify output format for snakemake output
#19
ilibarra
opened
1 year ago
1
Total counts per column in each query
#18
ilibarra
opened
1 year ago
1
Reduce complexity of the function mb.tl.train_iterative
#17
ilibarra
opened
1 year ago
1
Include publication/dataset cases to pipeline by name
#16
ilibarra
opened
1 year ago
0
Merge analysis-pipeline to development
#15
ege-erdogan
closed
1 year ago
1
add r2 columns to metrics output
#14
ege-erdogan
closed
1 year ago
5
include notebooks/pipeline/data_analysis.ipynb to pipeline
#13
ilibarra
opened
1 year ago
0
Verify config_test.yaml with PBM data
#12
ilibarra
closed
1 year ago
0
Update output to multiple columns
#11
ilibarra
opened
1 year ago
0
n_kernels not separated into multiple runs during fit_model.py
#10
ilibarra
closed
1 year ago
2
updates in pipeline to handle PBM datasets (UniProbe).
#9
ilibarra
closed
1 year ago
0
Run with variable epochs e.g. [10, 100, 200] and save output as a single row per n_epochs in metrics.tsv
#8
ilibarra
opened
1 year ago
0
Fetaure/tests
#7
ilibarra
closed
1 year ago
1
Training with simulated data & n_kernels as hyperparameter
#6
ege-erdogan
closed
1 year ago
1
n_kernels needs to be a hyperparameter similar to lr and n_epochs
#5
ilibarra
opened
1 year ago
0
Include simulated SELEX data to pipeline
#4
ilibarra
opened
1 year ago
0
updating config.yaml and typos
#3
ilibarra
closed
1 year ago
0
Merge branch development to main
#2
ege-erdogan
closed
1 year ago
0
Variable learning rate / batch size
#1
ilibarra
closed
1 year ago
0