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omnipathr-log/
raw_data/
results/method_comparison/compare_algorithms/Lasry/CPDB/samples_DEGs/**
results/method_comparison/compare_algorithms/Lasry/CPDB/samples_DEGs/*.tsv
results/method_comparison/compare_algorithms/Lasry/CPDB/samples_DEGs/*/*
results/method_comparison/compare_algorithms/Similie/CPDB/samples_DEGs/**
results/method_comparison/compare_algorithms/Similie/CPDB/samples_DEGs/*.tsv
results/method_comparison/compare_algorithms/Similie/CPDB/samples_DEGs/*/*
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/**
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/*.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/*/*
.git/objects/pack/pack-5257edbf585b656d88089dda26fca7508ec0110d.pack
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/AML-0024_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/healthy-4_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/healthy-3_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/healthy-4003_counts.tsv
results/data_preprocessing/vanGalen_Hourigan/batch_corrected/adata_afterCorrection.h5ad
results/data_preprocessing/vanGalen_Hourigan/batch_corrected/counts_corr.csv.gz
results/data_preprocessing/Lasry/batch_corrected/counts_norm.mtx
results/data_preprocessing/Lasry/batch_corrected/counts_corr.csv.gz
results/data_preprocessing/Lasry/batch_corrected/lasry_batch_corr.csv.gz
results/data_preprocessing/Lasry/batch_corrected/lasry_corr_norm.pickle
.git/objects/pack/pack-5257edbf585b656d88089dda26fca7508ec0110d.pack
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/AML-0024_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/AML-3133_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/healthy-5_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/AML-1371_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/AML-0693_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/healthy-4_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/AML-0160_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/healthy-2_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/healthy-3_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/healthy-1_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/healthy-4003_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/AML-4340_counts.tsv
results/data_preprocessing/vanGalen_Hourigan/batch_corrected/adata_afterCorrection.h5ad
results/data_preprocessing/vanGalen_Hourigan/batch_corrected/counts_corr.csv.gz
results/data_preprocessing/Lasry/batch_corrected/counts_norm.mtx
results/data_preprocessing/Lasry/batch_corrected/counts_corr.csv.gz
results/data_preprocessing/Lasry/batch_corrected/lasry_batch_corr.csv.gz
results/data_preprocessing/Lasry/batch_corrected/lasry_corr_norm.pickle
.git/objects/pack/pack-5257edbf585b656d88089dda26fca7508ec0110d.pack
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/AML-0024_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/AML-3133_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/healthy-5_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/AML-1371_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/AML-0693_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/healthy-4_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/AML-0160_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/healthy-2_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/healthy-3_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/healthy-1_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/healthy-4003_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/AML-4340_counts.tsv
results/data_preprocessing/vanGalen_Hourigan/batch_corrected/adata_afterCorrection.h5ad
results/data_preprocessing/vanGalen_Hourigan/batch_corrected/counts_corr.csv.gz
results/data_preprocessing/Lasry/batch_corrected/counts_norm.mtx
results/data_preprocessing/Lasry/batch_corrected/counts_corr.csv.gz
results/data_preprocessing/Lasry/batch_corrected/lasry_batch_corr.csv.gz
results/data_preprocessing/Lasry/batch_corrected/lasry_corr_norm.pickle
.git/objects/pack/pack-5257edbf585b656d88089dda26fca7508ec0110d.pack
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/AML-0024_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/AML-3133_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/healthy-5_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/AML-1371_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/AML-0693_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/healthy-4_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/AML-0160_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/healthy-2_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/healthy-3_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/healthy-1_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/healthy-4003_counts.tsv
results/method_comparison/compare_algorithms/CPDB/samples_DEGs/AML-4340_counts.tsv
results/data_preprocessing/vanGalen_Hourigan/batch_corrected/adata_afterCorrection.h5ad
results/data_preprocessing/vanGalen_Hourigan/batch_corrected/counts_corr.csv.gz
results/data_preprocessing/Lasry/batch_corrected/counts_norm.mtx
results/data_preprocessing/Lasry/batch_corrected/counts_corr.csv.gz
results/data_preprocessing/Lasry/batch_corrected/lasry_batch_corr.csv.gz
results/data_preprocessing/Lasry/batch_corrected/lasry_corr_norm.pickle
results/method_comparison/compare_algorithms/Lasry/CPDB/samples_DEGs/AML-0160_counts.tsv
results/method_comparison/compare_algorithms/Lasry/CPDB/samples_DEGs/AML-3133_counts.tsv
results/method_comparison/compare_algorithms/Lasry/CPDB/samples_DEGs/healthy-1_counts.tsv
results/method_comparison/compare_algorithms/Lasry/CPDB/samples_DEGs/healthy-4003_counts.tsv
results/method_comparison/compare_algorithms/Lasry/CPDB/samples_DEGs/AML-0024_counts.tsv
results/method_comparison/compare_algorithms/Lasry/CPDB/samples_DEGs/AML-0693_counts.tsv
results/method_comparison/compare_algorithms/Lasry/CPDB/samples_DEGs/healthy-5_counts.tsv
results/method_comparison/compare_algorithms/Lasry/CPDB/samples_DEGs/healthy-2_counts.tsv
results/method_comparison/compare_algorithms/Lasry/CPDB/samples_DEGs/AML-4340_counts.tsv
results/method_comparison/compare_algorithms/Lasry/CPDB/samples_DEGs/AML-1371_counts.tsv
results/method_comparison/compare_algorithms/Lasry/CPDB/samples_DEGs/healthy-3_counts.tsv
results/method_comparison/compare_algorithms/Lasry/CPDB/samples_DEGs/healthy-4_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/BM-B_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/BM-W_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/BM-P_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/BM-L_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/BM-M_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/BM-K_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/AML328-D0_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/AML1012-D0_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/AML707B-D0_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/AML556-D0_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/BM-H_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/BM-U_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/BM-O_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/BM-C1_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/BM-E_counts.tsv
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results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/BM-N_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/BM4_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/BM-Sk2_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/BM-R_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/BM-F_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/AML921A-D0_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/BM-Q_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/BM-A_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/BM-T_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/AML916-D0_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/BM-J_counts.tsv
results/method_comparison/compare_algorithms/vanGalen/CPDB/samples_DEGs/AML419A-D0_counts.tsv
results/method_comparison/compare_algorithms/Similie/community/interactions.RData
results/method_comparison/compare_algorithms/Similie/CPDB/samples_DEGs/N539.B_Inflamed_counts.tsv
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src/data_preprocessing/vanGalen_Hourigan/1.preprocess_data/outs/counts.RData
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data/Lasry/raw_data/GSE185381_RAW/GSM5613790_2021-03-09-Z-1-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613765_2020-01-03-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613777_2020-09-11-AML4340_AML1371-c1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613748_2019-08-01-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613760_2019-11-19-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613759_2019-11-04-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613770_2020-03-18-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613756_2019-10-25-count-5_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613779_2020-09-15-AML0024_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613745_2019-07-01-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613744_2019-07-01-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613762_2019-11-26-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613769_2020-03-18-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613775_2020-08-26-Control4003-c2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613788_2021-03-09-Z-1-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613787_2021-03-09-count1_0.95_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613789_2021-03-09-Z-1-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613757_2019-11-04-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613785_2021-03-09-AML3948_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613761_2019-11-19-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613778_2020-09-11-AML4340_AML1371-c2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613767_2020-03-18-AML0048-c2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613764_2020-01-03-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613774_2020-08-26-Control4003-c1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613786_2021-03-09-AMLMS3730_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613782_2020-10-06-count4_0.95_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613780_2020-10-06-AML4897_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613752_2019-08-29-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613766_2020-03-18-AML0048-c1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613751_2019-08-29-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613749_2019-08-01-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613746_2019-07-01-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613784_2021-03-09-AML0693_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613750_2019-08-01-count-4_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613763_2019-11-26-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613781_2020-10-06-count2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613758_2019-11-04-count-2_RNA_soupx_processed.csv
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3587990_AML921A-D0.dem.txt
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3587963_AML556-D0.dem.txt
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3587933_AML328-D113.dem.txt
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3588000_BM4.dem.txt
.git/objects/pack/pack-c65ac498033d4142d03a91967c677c367b8fceeb.pack
src/data_preprocessing/Lasry/2.filtering/outs/counts_norm.csv.gz
src/data_preprocessing/Lasry/2.filtering/outs/counts_norm.mtx
src/data_preprocessing/Lasry/3.UMAP/outs/counts_corr.csv.gz
src/data_preprocessing/Lasry/3.UMAP/lasry_batch_corr.csv.gz
src/data_preprocessing/Lasry/1.preprocess_data/outs/counts.RData
src/data_preprocessing/vanGalen_Hourigan/2.filtering/outs/counts_cf_ctf_gf_sf.RData
src/data_preprocessing/vanGalen_Hourigan/3.normalization/outs/counts_norm.mtx
src/data_preprocessing/vanGalen_Hourigan/1.preprocess_data/outs/counts.RData
src/data_preprocessing/vanGalen_Hourigan/4.1.batch_correction/adata_beforeCorrection.h5ad
src/data_preprocessing/vanGalen_Hourigan/4.1.batch_correction/outs/adata_afterCorrection.h5ad
src/data_preprocessing/vanGalen_Hourigan/4.1.batch_correction/outs/counts_corr.csv.gz
src/data_preprocessing/Smillie/1. Preprocessing/outs/counts.RData
data/Lasry/raw_data/GSE185381_RAW/GSM5613776_2020-08-26-Control4003-c3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613771_2020-03-18-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613790_2021-03-09-Z-1-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613765_2020-01-03-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613777_2020-09-11-AML4340_AML1371-c1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613748_2019-08-01-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613760_2019-11-19-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613759_2019-11-04-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613770_2020-03-18-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613756_2019-10-25-count-5_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613779_2020-09-15-AML0024_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613745_2019-07-01-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613744_2019-07-01-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613762_2019-11-26-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613769_2020-03-18-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613775_2020-08-26-Control4003-c2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613788_2021-03-09-Z-1-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613787_2021-03-09-count1_0.95_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613789_2021-03-09-Z-1-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613757_2019-11-04-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613785_2021-03-09-AML3948_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613761_2019-11-19-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613778_2020-09-11-AML4340_AML1371-c2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613767_2020-03-18-AML0048-c2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613764_2020-01-03-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613774_2020-08-26-Control4003-c1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613786_2021-03-09-AMLMS3730_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613782_2020-10-06-count4_0.95_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613780_2020-10-06-AML4897_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613752_2019-08-29-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613766_2020-03-18-AML0048-c1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613751_2019-08-29-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613749_2019-08-01-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613746_2019-07-01-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613784_2021-03-09-AML0693_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613750_2019-08-01-count-4_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613763_2019-11-26-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613781_2020-10-06-count2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613758_2019-11-04-count-2_RNA_soupx_processed.csv
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3587990_AML921A-D0.dem.txt
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3587963_AML556-D0.dem.txt
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3587933_AML328-D113.dem.txt
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3588000_BM4.dem.txt
data/Smillie/raw_data/gene_sorted-Fib.matrix.mtx
data/Smillie/raw_data/gene_sorted-Imm.matrix.mtx
data/Smillie/raw_data/gene_sorted-Epi.matrix.mtx
.git/objects/pack/pack-c65ac498033d4142d03a91967c677c367b8fceeb.pack
src/data_preprocessing/Lasry/2.filtering/outs/counts_norm.csv.gz
src/data_preprocessing/Lasry/2.filtering/outs/counts_norm2.csv.gz
src/data_preprocessing/Lasry/2.filtering/outs/counts_norm.mtx
src/data_preprocessing/Lasry/3.UMAP/outs/counts_corr.csv.gz
src/data_preprocessing/Lasry/3.UMAP/lasry_batch_corr.csv.gz
src/data_preprocessing/Lasry/1.preprocess_data/outs/counts.RData
src/data_preprocessing/vanGalen_Hourigan/2.filtering/outs/counts_cf_ctf_gf_sf.RData
src/data_preprocessing/vanGalen_Hourigan/3.normalization/outs/counts_norm.mtx
src/data_preprocessing/vanGalen_Hourigan/1.preprocess_data/outs/counts.RData
src/data_preprocessing/vanGalen_Hourigan/4.1.batch_correction/adata_beforeCorrection.h5ad
src/data_preprocessing/vanGalen_Hourigan/4.1.batch_correction/outs/adata_afterCorrection.h5ad
src/data_preprocessing/vanGalen_Hourigan/4.1.batch_correction/outs/counts_corr.csv.gz
src/data_preprocessing/Smillie/1. Preprocessing/outs/counts.RData
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-0160_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-3133_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-1_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-4003_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-0024_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-0693_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-5_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-2_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-4340_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-1371_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-3_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-4_counts.tsv
data/Lasry/raw_data/GSE185381_RAW/GSM5613776_2020-08-26-Control4003-c3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613771_2020-03-18-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613790_2021-03-09-Z-1-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613765_2020-01-03-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613777_2020-09-11-AML4340_AML1371-c1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613748_2019-08-01-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613760_2019-11-19-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613759_2019-11-04-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613770_2020-03-18-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613756_2019-10-25-count-5_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613779_2020-09-15-AML0024_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613745_2019-07-01-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613744_2019-07-01-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613762_2019-11-26-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613769_2020-03-18-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613775_2020-08-26-Control4003-c2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613788_2021-03-09-Z-1-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613787_2021-03-09-count1_0.95_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613789_2021-03-09-Z-1-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613757_2019-11-04-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613785_2021-03-09-AML3948_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613761_2019-11-19-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613778_2020-09-11-AML4340_AML1371-c2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613767_2020-03-18-AML0048-c2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613764_2020-01-03-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613774_2020-08-26-Control4003-c1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613786_2021-03-09-AMLMS3730_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613782_2020-10-06-count4_0.95_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613780_2020-10-06-AML4897_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613752_2019-08-29-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613766_2020-03-18-AML0048-c1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613751_2019-08-29-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613749_2019-08-01-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613746_2019-07-01-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613784_2021-03-09-AML0693_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613750_2019-08-01-count-4_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613763_2019-11-26-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613781_2020-10-06-count2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613758_2019-11-04-count-2_RNA_soupx_processed.csv
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3587990_AML921A-D0.dem.txt
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3587963_AML556-D0.dem.txt
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3587933_AML328-D113.dem.txt
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3588000_BM4.dem.txt
data/Smillie/raw_data/gene_sorted-Fib.matrix.mtx
data/Smillie/raw_data/gene_sorted-Imm.matrix.mtx
data/Smillie/raw_data/gene_sorted-Epi.matrix.mtx
.git/objects/pack/pack-c65ac498033d4142d03a91967c677c367b8fceeb.pack
src/data_preprocessing/Lasry/2.filtering/outs/counts_norm.csv.gz
src/data_preprocessing/Lasry/2.filtering/outs/counts_norm2.csv.gz
src/data_preprocessing/Lasry/2.filtering/outs/counts_norm.mtx
src/data_preprocessing/Lasry/3.UMAP/outs/counts_corr.csv.gz
src/data_preprocessing/Lasry/3.UMAP/lasry_batch_corr.csv.gz
src/data_preprocessing/Lasry/1.preprocess_data/outs/counts.RData
src/data_preprocessing/vanGalen_Hourigan/2.filtering/outs/counts_cf_ctf_gf_sf.RData
src/data_preprocessing/vanGalen_Hourigan/3.normalization/outs/counts_norm.mtx
src/data_preprocessing/vanGalen_Hourigan/1.preprocess_data/outs/counts.RData
src/data_preprocessing/vanGalen_Hourigan/4.1.batch_correction/adata_beforeCorrection.h5ad
src/data_preprocessing/vanGalen_Hourigan/4.1.batch_correction/outs/adata_afterCorrection.h5ad
src/data_preprocessing/vanGalen_Hourigan/4.1.batch_correction/outs/counts_corr.csv.gz
src/data_preprocessing/Smillie/1. Preprocessing/outs/counts.RData
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-0160_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-3133_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-1_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-4003_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-0024_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-0693_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-5_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-2_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-4340_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-1371_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-3_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-4_counts.tsv
data/Lasry/raw_data/GSE185381_RAW/GSM5613776_2020-08-26-Control4003-c3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613771_2020-03-18-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613790_2021-03-09-Z-1-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613765_2020-01-03-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613777_2020-09-11-AML4340_AML1371-c1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613748_2019-08-01-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613760_2019-11-19-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613759_2019-11-04-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613770_2020-03-18-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613756_2019-10-25-count-5_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613779_2020-09-15-AML0024_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613745_2019-07-01-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613744_2019-07-01-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613762_2019-11-26-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613769_2020-03-18-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613775_2020-08-26-Control4003-c2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613788_2021-03-09-Z-1-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613787_2021-03-09-count1_0.95_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613789_2021-03-09-Z-1-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613757_2019-11-04-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613785_2021-03-09-AML3948_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613761_2019-11-19-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613778_2020-09-11-AML4340_AML1371-c2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613767_2020-03-18-AML0048-c2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613764_2020-01-03-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613774_2020-08-26-Control4003-c1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613786_2021-03-09-AMLMS3730_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613782_2020-10-06-count4_0.95_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613780_2020-10-06-AML4897_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613752_2019-08-29-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613766_2020-03-18-AML0048-c1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613751_2019-08-29-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613749_2019-08-01-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613746_2019-07-01-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613784_2021-03-09-AML0693_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613750_2019-08-01-count-4_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613763_2019-11-26-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613781_2020-10-06-count2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613758_2019-11-04-count-2_RNA_soupx_processed.csv
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3587990_AML921A-D0.dem.txt
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3587963_AML556-D0.dem.txt
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3587933_AML328-D113.dem.txt
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3588000_BM4.dem.txt
data/Smillie/raw_data/gene_sorted-Fib.matrix.mtx
data/Smillie/raw_data/gene_sorted-Imm.matrix.mtx
data/Smillie/raw_data/gene_sorted-Epi.matrix.mtx
.git/objects/pack/pack-c65ac498033d4142d03a91967c677c367b8fceeb.pack
src/data_preprocessing/Lasry/2.filtering/outs/counts_norm.csv.gz
src/data_preprocessing/Lasry/2.filtering/outs/counts_norm2.csv.gz
src/data_preprocessing/Lasry/2.filtering/outs/counts_norm.mtx
src/data_preprocessing/Lasry/3.UMAP/outs/counts_corr.csv.gz
src/data_preprocessing/Lasry/3.UMAP/lasry_batch_corr.csv.gz
src/data_preprocessing/Lasry/1.preprocess_data/outs/counts.RData
src/data_preprocessing/vanGalen_Hourigan/2.filtering/outs/counts_cf_ctf_gf_sf.RData
src/data_preprocessing/vanGalen_Hourigan/3.normalization/outs/counts_norm.mtx
src/data_preprocessing/vanGalen_Hourigan/1.preprocess_data/outs/counts.RData
src/data_preprocessing/vanGalen_Hourigan/4.1.batch_correction/adata_beforeCorrection.h5ad
src/data_preprocessing/vanGalen_Hourigan/4.1.batch_correction/outs/adata_afterCorrection.h5ad
src/data_preprocessing/vanGalen_Hourigan/4.1.batch_correction/outs/counts_corr.csv.gz
src/data_preprocessing/Smillie/1. Preprocessing/outs/counts.RData
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-0160_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-3133_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-1_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-4003_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-0024_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-0693_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-5_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-2_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-4340_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-1371_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-3_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-4_counts.tsv
data/Lasry/raw_data/GSE185381_RAW/GSM5613776_2020-08-26-Control4003-c3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613771_2020-03-18-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613790_2021-03-09-Z-1-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613765_2020-01-03-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613777_2020-09-11-AML4340_AML1371-c1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613748_2019-08-01-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613760_2019-11-19-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613759_2019-11-04-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613770_2020-03-18-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613756_2019-10-25-count-5_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613779_2020-09-15-AML0024_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613745_2019-07-01-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613744_2019-07-01-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613762_2019-11-26-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613769_2020-03-18-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613775_2020-08-26-Control4003-c2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613788_2021-03-09-Z-1-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613787_2021-03-09-count1_0.95_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613789_2021-03-09-Z-1-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613757_2019-11-04-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613785_2021-03-09-AML3948_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613761_2019-11-19-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613778_2020-09-11-AML4340_AML1371-c2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613767_2020-03-18-AML0048-c2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613764_2020-01-03-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613774_2020-08-26-Control4003-c1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613786_2021-03-09-AMLMS3730_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613782_2020-10-06-count4_0.95_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613780_2020-10-06-AML4897_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613752_2019-08-29-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613766_2020-03-18-AML0048-c1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613751_2019-08-29-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613749_2019-08-01-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613746_2019-07-01-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613784_2021-03-09-AML0693_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613750_2019-08-01-count-4_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613763_2019-11-26-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613781_2020-10-06-count2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613758_2019-11-04-count-2_RNA_soupx_processed.csv
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3587990_AML921A-D0.dem.txt
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3587963_AML556-D0.dem.txt
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3587933_AML328-D113.dem.txt
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3588000_BM4.dem.txt
data/Smillie/raw_data/gene_sorted-Fib.matrix.mtx
data/Smillie/raw_data/gene_sorted-Imm.matrix.mtx
data/Smillie/raw_data/gene_sorted-Epi.matrix.mtx
.git/objects/pack/pack-c65ac498033d4142d03a91967c677c367b8fceeb.pack
src/data_preprocessing/Lasry/2.filtering/outs/counts_norm.csv.gz
src/data_preprocessing/Lasry/2.filtering/outs/counts_norm.mtx
src/data_preprocessing/Lasry/3.UMAP/outs/counts_corr.csv.gz
src/data_preprocessing/Lasry/3.UMAP/lasry_batch_corr.csv.gz
src/data_preprocessing/Lasry/1.preprocess_data/outs/counts.RData
src/data_preprocessing/vanGalen_Hourigan/2.filtering/outs/counts_cf_ctf_gf_sf.RData
src/data_preprocessing/vanGalen_Hourigan/3.normalization/outs/counts_norm.mtx
src/data_preprocessing/vanGalen_Hourigan/1.preprocess_data/outs/counts.RData
src/data_preprocessing/vanGalen_Hourigan/4.1.batch_correction/adata_beforeCorrection.h5ad
src/data_preprocessing/vanGalen_Hourigan/4.1.batch_correction/outs/adata_afterCorrection.h5ad
src/data_preprocessing/vanGalen_Hourigan/4.1.batch_correction/outs/counts_corr.csv.gz
src/data_preprocessing/Smillie/1. Preprocessing/outs/counts.RData
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-0160_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-3133_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-1_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-4003_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-0024_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-0693_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-5_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-2_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-4340_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-1371_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-3_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-4_counts.tsv
data/Lasry/raw_data/GSE185381_RAW/GSM5613776_2020-08-26-Control4003-c3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613771_2020-03-18-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613790_2021-03-09-Z-1-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613765_2020-01-03-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613777_2020-09-11-AML4340_AML1371-c1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613748_2019-08-01-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613760_2019-11-19-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613759_2019-11-04-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613770_2020-03-18-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613756_2019-10-25-count-5_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613779_2020-09-15-AML0024_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613745_2019-07-01-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613744_2019-07-01-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613762_2019-11-26-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613769_2020-03-18-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613775_2020-08-26-Control4003-c2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613788_2021-03-09-Z-1-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613787_2021-03-09-count1_0.95_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613789_2021-03-09-Z-1-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613757_2019-11-04-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613785_2021-03-09-AML3948_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613761_2019-11-19-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613778_2020-09-11-AML4340_AML1371-c2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613767_2020-03-18-AML0048-c2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613764_2020-01-03-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613774_2020-08-26-Control4003-c1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613786_2021-03-09-AMLMS3730_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613782_2020-10-06-count4_0.95_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613780_2020-10-06-AML4897_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613752_2019-08-29-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613766_2020-03-18-AML0048-c1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613751_2019-08-29-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613749_2019-08-01-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613746_2019-07-01-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613784_2021-03-09-AML0693_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613750_2019-08-01-count-4_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613763_2019-11-26-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613781_2020-10-06-count2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613758_2019-11-04-count-2_RNA_soupx_processed.csv
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3587990_AML921A-D0.dem.txt
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3587963_AML556-D0.dem.txt
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3587933_AML328-D113.dem.txt
data/vanGalen_Hourigan/raw_data/GSE116256_RAW/GSM3588000_BM4.dem.txt
data/Smillie/raw_data/gene_sorted-Fib.matrix.mtx
data/Smillie/raw_data/gene_sorted-Imm.matrix.mtx
data/Smillie/raw_data/gene_sorted-Epi.matrix.mtx
.git/objects/pack/pack-c65ac498033d4142d03a91967c677c367b8fceeb.pack
src/data_preprocessing/Lasry/2.filtering/outs/counts_norm.csv.gz
src/data_preprocessing/Lasry/2.filtering/outs/counts_norm.mtx
src/data_preprocessing/Lasry/3.UMAP/outs/counts_corr.csv.gz
src/data_preprocessing/Lasry/3.UMAP/lasry_batch_corr.csv.gz
src/data_preprocessing/Lasry/1.preprocess_data/outs/counts.RData
src/data_preprocessing/vanGalen_Hourigan/2.filtering/outs/counts_cf_ctf_gf_sf.RData
src/data_preprocessing/vanGalen_Hourigan/3.normalization/outs/counts_norm.mtx
src/data_preprocessing/vanGalen_Hourigan/1.preprocess_data/outs/counts.RData
src/data_preprocessing/vanGalen_Hourigan/4.1.batch_correction/adata_beforeCorrection.h5ad
src/data_preprocessing/vanGalen_Hourigan/4.1.batch_correction/outs/adata_afterCorrection.h5ad
src/data_preprocessing/vanGalen_Hourigan/4.1.batch_correction/outs/counts_corr.csv.gz
src/data_preprocessing/Smillie/1. Preprocessing/outs/counts.RData
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-0160_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-3133_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-1_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-4003_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-0024_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-0693_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-5_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-2_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-4340_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/AML-1371_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-3_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_CellPhoneDB/run_algorithm/outs/samples_DEGs/healthy-4_counts.tsv
src/method_comparison/compare_algorithms/prepare_data/run_NicheNet/build_customDB/NNET_Custom/Optimization_results.rds
data/Lasry/raw_data/GSE185381_RAW/GSM5613776_2020-08-26-Control4003-c3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613771_2020-03-18-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613790_2021-03-09-Z-1-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613765_2020-01-03-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613777_2020-09-11-AML4340_AML1371-c1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613748_2019-08-01-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613760_2019-11-19-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613759_2019-11-04-count-3_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613770_2020-03-18-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613756_2019-10-25-count-5_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613779_2020-09-15-AML0024_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613745_2019-07-01-count-2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613744_2019-07-01-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613762_2019-11-26-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613769_2020-03-18-count-1_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613775_2020-08-26-Control4003-c2_RNA_soupx_processed.csv
data/Lasry/raw_data/GSE185381_RAW/GSM5613788_2021-03-09-Z-1-1_RNA_soupx_processed.csv