This is a script repository for data analysis in the FMT-donor paper, "Donor-dependent fecal microbiota transplantation efficacy against necrotizing enterocolitis in preterm pigs". [Click me]
A tiny blog describing the main finding is posted on Nature Portfolio Microbiology Community. [Click me]
├── data
│ ├── BIN_REFINEMENT
│ │ ├── coASS
│ │ └── singleASSBIN
│ ├── coverm_genomewide
│ ├── desep2_kaiju
│ ├── panphlan
│ └── strainphlan
├── figure
├── scripts_sequencing
├── scripts_vis
└── table
data: metadata, processed output from script_sequencing, etc, are used for data visualization, generated tables
figure generated figures in the paper, png file
scripts_sequencing: processing code for sequencing data, and the working path is set accordingly on our sever
scripts_vis: codes for figures and tables
table: generated tables in the paper, tsv file
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Fig. 1 (Inserted barplot generated by scripts_vis/figure_1_barplot.R)
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Fig. 2 (Figure 2 generated by scripts_vis/figure_2.R)
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Fig. 3 (Figure 3 generated by scripts_vis/figure_3.R)
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Fig. 4 (Figure 4 generated by scripts_vis/figure_4.R)
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Fig. 5 (Figure 5 generated by scripts_vis/figure_5.R)
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Fig. 6 (Figure 6 generated by scripts_vis/figure_6.R)
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Fig. 7 Multi-panel figures was combined manually.
Fig. 7A generated by scripts_vis/figure_7A.R
Fig. 7B generated by scripts_vis/figure_7B.R
Fig. 7C generated by scripts_vis/figure_7C_table_s3.R
Fig. 7D generated by scripts_vis/virome.R -
Fig. S1 (Fig. S1 generated by scripts_vis/figure_s1_s2.R)
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Fig. S2 (Fig. S2 generated by scripts_vis/figure_s1_s2.R)
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Fig. S3 (Fig. S3 generated by scripts_vis/figure_s3.R)
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Fig. S4 (Fig. S4 generated by scripts_vis/figure_s4.R)
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Fig. S5 (Fig. S5 generated by scripts_vis/figure_s5.R)
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Fig. S6 (Fig. S6 generated by scripts_vis/figure_s6.R)
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Fig. S7 (Fig. S7 generated by MAGpy utilities scripts_sequencing/MAGpy.sh)
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Fig. S8 generated with the help of scripts_vis/virome.R and cytoscape
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Fig. S9 composed of several histological photos
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Fig. S10 (Fig. S10 was drawn manually)
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Table 1 (Table 1 generated by scripts_vis/table_1.R)
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Table S1 and S2 (Table S1 and Table s2 generated by scripts_vis/table_s1_s2.R)
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Table S3 (Table S3 generated by scripts_vis/figure_7C_table_s3_s4.R)
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Table S4 (Table S4 generated by scripts_vis/figure_7C_table_s3_s4.R)
