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.gitignore
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data/chrominfo.snp6.hg19.RData
data/AnnotationData/Encode_replication_timing.tsv
.gitignore
data/AnnotationData/gap_hg19.txt
data/AnnotationData/chrominfo.snp6.txt
data/AnnotationData/filteredAscat.txt
data/AnnotationData/gc.content.txt
data/AnnotationData/hg19.chrom.sizes.txt
data/AnnotationData/mateo_hg19_chromsizes.txt
data/AnnotationData/repeats
data/AnnotationData/wgEncodeUwRepliSeqGm12878WaveSignalRep1.bw
core.8521
core.9666
core.32869
.gitignore
core.34374
.gitignore
data/chrominfo.snp6.txt
data/Encode_replication_timing.tsv
data/filteredAscat.txt
data/gap_hg19.txt
data/gc.content.txt
data/hg19.chrom.sizes.txt
data/mateo_hg19_chromsizes.txt
data/repeats
data/wgEncodeUwRepliSeqGm12878WaveSignalRep1.bw
.gwf/update
scripts/.gwf/update
scripts/.gwf/logs/create_features.stderr
scripts/.gwf/logs/create_features.stdout
scripts/modpath.py
scripts/__pycache__/modpath.cpython-38.pyc
steps/test_features_mateo_10.txt
data/gc_content.txt
scripts/__pycache__/workflow.cpython-38.pyc
scripts/__pycache__/workflow.cpython-38.pyc
scripts/__pycache__/feature_func.cpython-38.pyc
scripts/__pycache__/create_feature_file.cpython-38.pyc
scripts/__pycache__/feature_func.cpython-38.pyc
scripts/__pycache__/feature_func.cpython-38.pyc
scripts/.gwf/slurm-backend-tracked.json
scripts/__pycache__/feature_func.cpython-38.pyc
data/TCGA-02-0001.segments.raw.txt
scripts/filteredoff.txt
scripts/temp.py
scripts/.gwf/logs/CreateFeatures.stderr
scripts/.gwf/logs/CreateFeatures.stdout
scripts/.gwf/logs/UpdateAscat.stderr
scripts/.gwf/logs/UpdateAscat.stdout
scripts/__pycache__/feature_func.cpython-38.pyc
steps/discrete.txt
data/filteredAscatRaw.txt
figures/optimalalpha_10.pdf
steps/sampled_0.7.ascat
steps/gensim/hdp/hdp_f10.model
steps/gensim/hdp/hdp_f10.model.lda_beta.npy
steps/gensim/hdp/hdp_f10.model.m_Elogbeta.npy
steps/gensim/hdp/hdp_f10.model.m_lambda.npy
steps/gensim/hdp/hdp_f10.model
steps/gensim/hdp/hdp_f10.model
steps/gensim/nmf/nmf_t10_f10.model
steps/gensim/nmf/nmf_t11_f10.model
steps/gensim/nmf/nmf_t12_f10.model
steps/gensim/nmf/nmf_t13_f10.model
steps/gensim/nmf/nmf_t14_f10.model
steps/gensim/nmf/nmf_t15_f10.model
steps/gensim/nmf/nmf_t16_f10.model
steps/gensim/nmf/nmf_t17_f10.model
steps/gensim/nmf/nmf_t18_f10.model
steps/gensim/nmf/nmf_t19_f10.model
steps/gensim/nmf/nmf_t9_f10.model
steps/gensim/nmf/nmf_t15_f10.model
steps/gensim/nmf/nmf_t9_f10.model
steps/gensim/nmf/nmf_t10_f10.model
steps/gensim/nmf/nmf_t11_f10.model
steps/gensim/nmf/nmf_t12_f10.model
steps/gensim/nmf/nmf_t13_f10.model
steps/gensim/nmf/nmf_t14_f10.model
steps/gensim/nmf/nmf_t15_f10.model
steps/gensim/nmf/nmf_t16_f10.model
steps/gensim/nmf/nmf_t17_f10.model
steps/gensim/nmf/nmf_t18_f10.model
steps/gensim/nmf/nmf_t19_f10.model
data/all_muts_pass_and_polyphen.txt
data/all_tcga_gene_exp.txt
data/all_tcga_cin_measures.txt
data/all_tcga_maf_summary.txt
data/all_tcga_maf.txt
data/sanchez_vega_pws_1026.csv
data/cin_locations.txt
data/test.txt
<<<<<<< Updated upstream
=======
<<<<<<< Updated upstream
=======
scripts/.gwf/logs/gensimLDA_t1_f10.stderr
scripts/.gwf/logs/gensimLDA_t1_f10.stdout
scripts/.gwf/logs/gensimLDA_t2_f10.stderr
scripts/.gwf/logs/gensimLDA_t2_f10.stdout
scripts/.gwf/logs/gensimLDA_t3_f10.stderr
scripts/.gwf/logs/gensimLDA_t3_f10.stdout
scripts/.gwf/logs/gensimLDA_t4_f10.stderr
scripts/.gwf/logs/gensimLDA_t4_f10.stdout
scripts/.gwf/logs/gensimLDA_t5_f10.stderr
scripts/.gwf/logs/gensimLDA_t5_f10.stdout
scripts/.gwf/logs/gensimLDA_t6_f10.stderr
scripts/.gwf/logs/gensimLDA_t6_f10.stdout
scripts/.gwf/logs/gensimLDA_t7_f10.stderr
scripts/.gwf/logs/gensimLDA_t7_f10.stdout
scripts/.gwf/logs/gensimLDA_t8_f10.stderr
scripts/.gwf/logs/gensimLDA_t8_f10.stdout
scripts/.gwf/logs/gensimLDA_t9_f10.stderr
scripts/.gwf/logs/gensimLDA_t9_f10.stdout
scripts/.gwf/logs/gensimLDA_t10_f10.stderr
scripts/.gwf/logs/gensimLDA_t10_f10.stdout
scripts/.gwf/logs/gensimLDA_t11_f10.stderr
scripts/.gwf/logs/gensimLDA_t11_f10.stdout
scripts/.gwf/logs/gensimLDA_t12_f10.stderr
scripts/.gwf/logs/gensimLDA_t12_f10.stdout
scripts/.gwf/logs/gensimLDA_t13_f10.stderr
scripts/.gwf/logs/gensimLDA_t13_f10.stdout
scripts/.gwf/logs/gensimLDA_t14_f10.stderr
scripts/.gwf/logs/gensimLDA_t14_f10.stdout
scripts/.gwf/logs/gensimLDA_t15_f10.stderr
scripts/.gwf/logs/gensimLDA_t15_f10.stdout
>>>>>>> Stashed changes
>>>>>>> Stashed changes
data/repeats.txt
steps/sampled_0.3.ascat
steps/sampled_0.1.ascat
steps/sampledascat/sampled_0.1.ascat
steps/sampledascat/sampled_0.3.ascat
steps/sampledascat/sampled_0.7.ascat
notebooks/.ipynb_checkpoints/top1000-checkpoint.txt
notebooks/top1000.txt