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data
data
 
 
notebooks
notebooks
 
 
simulated
simulated
 
 
src/ABaCo
src/ABaCo
 
 
.DS_Store
.DS_Store
 
 
.gitignore
.gitignore
 
 
ABaCo_legacy.py
ABaCo_legacy.py
 
 
DGD-ABaCo.ipynb
DGD-ABaCo.ipynb
 
 
MetaABaCo.py
MetaABaCo.py
 
 
README.md
README.md
 
 
abaco_dlr_loop.py
abaco_dlr_loop.py
 
 
ad_count_batch_correct_batch.png
ad_count_batch_correct_batch.png
 
 
ad_count_batch_correct_bio.png
ad_count_batch_correct_bio.png
 
 
ad_count_prior_batch.png
ad_count_prior_batch.png
 
 
ad_count_prior_bio.png
ad_count_prior_bio.png
 
 
ad_count_sanity_check.py
ad_count_sanity_check.py
 
 
ad_count_sanity_check_ensemble.py
ad_count_sanity_check_ensemble.py
 
 
all_data_multi_run.py
all_data_multi_run.py
 
 
all_data_normal_run.py
all_data_normal_run.py
 
 
all_data_run.ipynb
all_data_run.ipynb
 
 
batch_loop.py
batch_loop.py
 
 
consistency.png
consistency.png
 
 
dtu-ge_batch_loop.py
dtu-ge_batch_loop.py
 
 
dtu_batch_correct_batch.png
dtu_batch_correct_batch.png
 
 
dtu_batch_correct_bio.png
dtu_batch_correct_bio.png
 
 
dtu_prior_batch.png
dtu_prior_batch.png
 
 
dtu_prior_bio.png
dtu_prior_bio.png
 
 
environment.yml
environment.yml
 
 
ibd_batch_correct_batch.png
ibd_batch_correct_batch.png
 
 
ibd_batch_correct_bio.png
ibd_batch_correct_bio.png
 
 
ibd_batch_loop.py
ibd_batch_loop.py
 
 
ibd_conqur.csv
ibd_conqur.csv
 
 
ibd_prior_batch.png
ibd_prior_batch.png
 
 
ibd_prior_bio.png
ibd_prior_bio.png
 
 
loop_train.py
loop_train.py
 
 
meta_abaco.ipynb
meta_abaco.ipynb
 
 
metarun.py
metarun.py
 
 
multi_run_results.ipynb
multi_run_results.ipynb
 
 
new_tools.ipynb
new_tools.ipynb
 
 
output.png
output.png
 
 
pcoa_ad_batch.png
pcoa_ad_batch.png
 
 
pcoa_ad_bio.png
pcoa_ad_bio.png
 
 
performance.ipynb
performance.ipynb
 
 
performance_all.png
performance_all.png
 
 
performance_batch.png
performance_batch.png
 
 
performance_prior.png
performance_prior.png
 
 
prior_train.py
prior_train.py
 
 
results_report.ipynb
results_report.ipynb
 
 
robustness.ipynb
robustness.ipynb
 
 
robustness.py
robustness.py
 
 
robustness_AD_count_abaco_vmm_kl.xlsx
robustness_AD_count_abaco_vmm_kl.xlsx
 
 
robustness_AD_count_abaco_vmm_no.xlsx
robustness_AD_count_abaco_vmm_no.xlsx
 
 
robustness_DTU-GE_abaco_std_kl.xlsx
robustness_DTU-GE_abaco_std_kl.xlsx
 
 
robustness_DTU-GE_abaco_std_no.xlsx
robustness_DTU-GE_abaco_std_no.xlsx
 
 
robustness_IBD_abaco_std_kl.xlsx
robustness_IBD_abaco_std_kl.xlsx
 
 
robustness_IBD_abaco_std_no.xlsx
robustness_IBD_abaco_std_no.xlsx
 
 
test.csv
test.csv
 
 
test_run.ipynb
test_run.ipynb
 
 
train_abaco_dtu.ipynb
train_abaco_dtu.ipynb
 
 
train_abaco_two_step.ipynb
train_abaco_two_step.ipynb
 
 
train_ad_count.ipynb
train_ad_count.ipynb
 
 
train_ibd_data.ipynb
train_ibd_data.ipynb
 
 
train_mgnify.ipynb
train_mgnify.ipynb
 
 
train_mog_prior.ipynb
train_mog_prior.ipynb
 
 
train_mog_prior_edited.ipynb
train_mog_prior_edited.ipynb
 
 
train_normal_prior.ipynb
train_normal_prior.ipynb
 
 
train_sponge.ipynb
train_sponge.ipynb
 
 

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BECA

Batch Effect Correction framework for metagenomic data.

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Batch Effect Correction framework for metagenomic data.

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