GitHub - zhenghaihui315/2020-NGSInfectedBodyFluids: scripts and data for Gu et al Nature Medicine 2020 manuscript

Name		Name	Last commit message	Last commit date
Latest commit History 2 Commits
264-545LenIlluminaDis.pdf		264-545LenIlluminaDis.pdf
BF-15-343-load2-dm.Candida_albicans.times		BF-15-343-load2-dm.Candida_albicans.times
BF-15-343-load2-dm.Enterococcus_faecium.times		BF-15-343-load2-dm.Enterococcus_faecium.times
BF-502-1.5m.Aspergillus_fumigatus.times		BF-502-1.5m.Aspergillus_fumigatus.times
BF-502-1.5m.Aspergillus_terreus.times		BF-502-1.5m.Aspergillus_terreus.times
BF15-264-1m.demultiplexed.all.times		BF15-264-1m.demultiplexed.all.times
BF264-1m.demultiplexed.Klebsiella_pneumoniae.times		BF264-1m.demultiplexed.Klebsiella_pneumoniae.times
BF406-1m.Mycoplasma_hominis.times		BF406-1m.Mycoplasma_hominis.times
BF545-1.5m.Klebsiella_aerogenes.times		BF545-1.5m.Klebsiella_aerogenes.times
ROC-rd5v1-BacTrain-HitThreshold.pdf		ROC-rd5v1-BacTrain-HitThreshold.pdf
ROC-rd5v1-BacTrain-OnOffGenusFamilyFilter.pdf		ROC-rd5v1-BacTrain-OnOffGenusFamilyFilter.pdf
ROC-rd5v1-BacTrain-OnOffNormalization.pdf		ROC-rd5v1-BacTrain-OnOffNormalization.pdf
ROC-rd5v1-BacTrain-TopOrg.pdf		ROC-rd5v1-BacTrain-TopOrg.pdf
ROC-rd5v1-FungalTrain-OnOffNormalization.pdf		ROC-rd5v1-FungalTrain-OnOffNormalization.pdf
ROC-rd5v1-FungalTrain-VaryReads.pdf		ROC-rd5v1-FungalTrain-VaryReads.pdf
ROC-rd5v2-subtypes.pdf		ROC-rd5v2-subtypes.pdf
ROCraw_df-rd5-NPv1Val-1read-Fun.csv		ROCraw_df-rd5-NPv1Val-1read-Fun.csv
ROCraw_df-rd5-NPv3ValidateOrig-Bac.csv		ROCraw_df-rd5-NPv3ValidateOrig-Bac.csv
ROCraw_df-rd5-v3ValOrig-Bac.csv		ROCraw_df-rd5-v3ValOrig-Bac.csv
ROCraw_df-rd5-v3ValOrig-Fun-1read.csv		ROCraw_df-rd5-v3ValOrig-Fun-1read.csv
RPM-CI-rd5-NPv3ValidateOrig-Bac.pdf		RPM-CI-rd5-NPv3ValidateOrig-Bac.pdf
RPMCompareIlNP-rd4V3-3.csv		RPMCompareIlNP-rd4V3-3.csv
RPMCompareIlNP-rd4V3.pdf		RPMCompareIlNP-rd4V3.pdf
RPMbyCultureColonies.pdf		RPMbyCultureColonies.pdf
RPMbyNPvsIll-bac.pdf		RPMbyNPvsIll-bac.pdf
RPMbySample-TN.pdf		RPMbySample-TN.pdf
RPMbySample.pdf		RPMbySample.pdf
S88.eps		S88.eps
S88.pdf		S88.pdf
Scripts for Gu, Deng, Lee et al. Nat Med 2020 "Rapid Pathogen Detection by Metagenomic Next-Generation Sequencing of Infected Body Fluids".ipynb		Scripts for Gu, Deng, Lee et al. Nat Med 2020 "Rapid Pathogen Detection by Metagenomic Next-Generation Sequencing of Infected Body Fluids".ipynb
bacHistoDis_df.pkl		bacHistoDis_df.pkl
bacHistoIllumina_df.pkl		bacHistoIllumina_df.pkl
bacHistoNanopore_df.pkl		bacHistoNanopore_df.pkl
contingencyTable_df-rd4-v7TrainVal-Plasma.csv		contingencyTable_df-rd4-v7TrainVal-Plasma.csv
contingencyTable_df-rd5-v1Train-Bac-1read.csv		contingencyTable_df-rd5-v1Train-Bac-1read.csv
contingencyTable_df-rd5-v1Train-Bac-2read.csv		contingencyTable_df-rd5-v1Train-Bac-2read.csv
contingencyTable_df-rd5-v1Train-Bac-4read.csv		contingencyTable_df-rd5-v1Train-Bac-4read.csv
contingencyTable_df-rd5-v1Train-Bac-5read.csv		contingencyTable_df-rd5-v1Train-Bac-5read.csv
contingencyTable_df-rd5-v1Train-Bac-genusFamOff.csv		contingencyTable_df-rd5-v1Train-Bac-genusFamOff.csv
contingencyTable_df-rd5-v1Train-Bac-normOff.csv		contingencyTable_df-rd5-v1Train-Bac-normOff.csv
contingencyTable_df-rd5-v1Train-Bac-topOrg10.csv		contingencyTable_df-rd5-v1Train-Bac-topOrg10.csv
contingencyTable_df-rd5-v1Train-Bac-topOrg3.csv		contingencyTable_df-rd5-v1Train-Bac-topOrg3.csv
contingencyTable_df-rd5-v1Train-Bac-topOrg7.csv		contingencyTable_df-rd5-v1Train-Bac-topOrg7.csv
contingencyTable_df-rd5-v1Train-Bac.csv		contingencyTable_df-rd5-v1Train-Bac.csv
contingencyTable_df-rd5-v1Train-Fun-1read.csv		contingencyTable_df-rd5-v1Train-Fun-1read.csv
contingencyTable_df-rd5-v1Train-Fun-2read.csv		contingencyTable_df-rd5-v1Train-Fun-2read.csv
contingencyTable_df-rd5-v1Train-Fun-3read.csv		contingencyTable_df-rd5-v1Train-Fun-3read.csv
contingencyTable_df-rd5-v1Train-Fun-normOff.csv		contingencyTable_df-rd5-v1Train-Fun-normOff.csv
contingencyTable_df-rd5-v2TrainVal-Bac-Abscess.csv		contingencyTable_df-rd5-v2TrainVal-Bac-Abscess.csv
contingencyTable_df-rd5-v2TrainVal-Bac-CSF.csv		contingencyTable_df-rd5-v2TrainVal-Bac-CSF.csv
contingencyTable_df-rd5-v2TrainVal-Bac-Joint.csv		contingencyTable_df-rd5-v2TrainVal-Bac-Joint.csv
contingencyTable_df-rd5-v2TrainVal-Bac-Peritoneal.csv		contingencyTable_df-rd5-v2TrainVal-Bac-Peritoneal.csv
contingencyTable_df-rd5-v2TrainVal-Bac-Pleural.csv		contingencyTable_df-rd5-v2TrainVal-Bac-Pleural.csv
contingencyTable_df-rd5-v2TrainVal-Bac.csv		contingencyTable_df-rd5-v2TrainVal-Bac.csv
cycleCorrectionRegression.pdf		cycleCorrectionRegression.pdf
fullGraphAll_df-rd5-v2TrainVal-Bac.csv		fullGraphAll_df-rd5-v2TrainVal-Bac.csv
fullGraph_df-rd4-NPv3TrainVal-Bac.csv		fullGraph_df-rd4-NPv3TrainVal-Bac.csv
fullGraph_df-rd4-v7TrainVal-Bac-100.csv		fullGraph_df-rd4-v7TrainVal-Bac-100.csv
fullGraph_df-rd4-v7TrainVal-Bac-colonyCount.csv		fullGraph_df-rd4-v7TrainVal-Bac-colonyCount.csv
fullGraph_df-rd5-v2TrainVal-Bac-colonyCount_EH.csv		fullGraph_df-rd5-v2TrainVal-Bac-colonyCount_EH.csv
fullGraph_df-rd5-v2TrainVal-Fun-1read.csv		fullGraph_df-rd5-v2TrainVal-Fun-1read.csv
fullGraph_df-rd5-v2TrainVal-Neg-Bac.csv		fullGraph_df-rd5-v2TrainVal-Neg-Bac.csv
fullGraph_df-rd5-v2TrainVal-Neg-Fun-1read.csv		fullGraph_df-rd5-v2TrainVal-Neg-Fun-1read.csv
fullGraph_df-rd5-v2TrainValPlasma-Bac-100.csv		fullGraph_df-rd5-v2TrainValPlasma-Bac-100.csv
funHisto_df.pkl		funHisto_df.pkl
histInsertSize-V1.py		histInsertSize-V1.py
humanHisto_df.pkl		humanHisto_df.pkl
lenBac.pdf		lenBac.pdf
lenBacFungi.pdf		lenBacFungi.pdf
nanoporeTTD.csv		nanoporeTTD.csv
nanoporeTTD.pdf		nanoporeTTD.pdf

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