Skip to content

Commit c0f7a47

Browse files
committed
Draft 1 of E coli growth curve analysis tutorial
First draft includes code to: merge well data and plate reader data, plot growth curves, calculate growth rates using the "growthrates" library, plot data distribution and boxplots and use a wilcoxen test to determine whether there is a significant difference between media. Code is interactive but questions / text are limited
1 parent aea8a1f commit c0f7a47

File tree

9 files changed

+825
-0
lines changed

9 files changed

+825
-0
lines changed

inst/growth_data.csv

Lines changed: 62 additions & 0 deletions
Large diffs are not rendered by default.

inst/resources/data/growth_data.csv

Lines changed: 62 additions & 0 deletions
Large diffs are not rendered by default.
Lines changed: 97 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,97 @@
1+
well,student,blank,media
2+
A1,NA,NA,NA
3+
A2,Student A,TRUE,LB
4+
A3,Student A,TRUE,LB
5+
A4,Student A,FALSE,LB
6+
A5,Student A,FALSE,LB
7+
A6,NA,NA,NA
8+
A7,Student B,TRUE,MM
9+
A8,Student B,TRUE,MM
10+
A9,Student B,FALSE,MM
11+
A10,Student B,FALSE,MM
12+
A11,NA,NA,NA
13+
A12,NA,NA,NA
14+
B1,NA,NA,NA
15+
B2,Student C,TRUE,LB
16+
B3,Student C,TRUE,LB
17+
B4,Student C,FALSE,LB
18+
B5,Student C,FALSE,LB
19+
B6,NA,NA,NA
20+
B7,Student D,TRUE,MM
21+
B8,Student D,TRUE,MM
22+
B9,Student D,FALSE,MM
23+
B10,Student D,FALSE,MM
24+
B11,NA,NA,NA
25+
B12,NA,NA,NA
26+
C1,NA,NA,NA
27+
C2,Student E,TRUE,LB
28+
C3,Student E,TRUE,LB
29+
C4,Student E,FALSE,LB
30+
C5,Student E,FALSE,LB
31+
C6,NA,NA,NA
32+
C7,Student F,TRUE,MM
33+
C8,Student F,TRUE,MM
34+
C9,Student F,FALSE,MM
35+
C10,Student F,FALSE,MM
36+
C11,NA,NA,NA
37+
C12,NA,NA,NA
38+
D1,NA,NA,NA
39+
D2,Student G,TRUE,LB
40+
D3,Student G,TRUE,LB
41+
D4,Student G,FALSE,LB
42+
D5,Student G,FALSE,LB
43+
D6,NA,NA,NA
44+
D7,Student H,TRUE,MM
45+
D8,Student H,TRUE,MM
46+
D9,Student H,FALSE,MM
47+
D10,Student H,FALSE,MM
48+
D11,NA,NA,NA
49+
D12,NA,NA,NA
50+
E1,NA,NA,NA
51+
E2,Student I,TRUE,LB
52+
E3,Student I,TRUE,LB
53+
E4,Student I,FALSE,LB
54+
E5,Student I,FALSE,LB
55+
E6,NA,NA,NA
56+
E7,Student J,TRUE,MM
57+
E8,Student J,TRUE,MM
58+
E9,Student J,FALSE,MM
59+
E10,Student J,FALSE,MM
60+
E11,NA,NA,NA
61+
E12,NA,NA,NA
62+
F1,NA,NA,NA
63+
F2,Student K,TRUE,LB
64+
F3,Student K,TRUE,LB
65+
F4,Student K,FALSE,LB
66+
F5,Student K,FALSE,LB
67+
F6,NA,NA,NA
68+
F7,Student L,TRUE,MM
69+
F8,Student L,TRUE,MM
70+
F9,Student L,FALSE,MM
71+
F10,Student L,FALSE,MM
72+
F11,NA,NA,NA
73+
F12,NA,NA,NA
74+
G1,NA,NA,NA
75+
G2,Student M,TRUE,LB
76+
G3,Student M,TRUE,LB
77+
G4,Student M,FALSE,LB
78+
G5,Student M,FALSE,LB
79+
G6,NA,NA,NA
80+
G7,Student N,TRUE,MM
81+
G8,Student N,TRUE,MM
82+
G9,Student N,FALSE,MM
83+
G10,Student N,FALSE,MM
84+
G11,NA,NA,NA
85+
G12,NA,NA,NA
86+
H1,NA,NA,NA
87+
H2,Student O,TRUE,LB
88+
H3,Student O,TRUE,LB
89+
H4,Student O,FALSE,LB
90+
H5,Student O,FALSE,LB
91+
H6,NA,NA,NA
92+
H7,Student P,TRUE,MM
93+
H8,Student P,TRUE,MM
94+
H9,Student P,FALSE,MM
95+
H10,Student P,FALSE,MM
96+
H11,NA,NA,NA
97+
H12,NA,NA,NA

inst/resources/images/growth_data.csv

Lines changed: 62 additions & 0 deletions
Large diffs are not rendered by default.
Lines changed: 97 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,97 @@
1+
well,student,blank,media
2+
A1,NA,NA,NA
3+
A2,Student A,TRUE,LB
4+
A3,Student A,TRUE,LB
5+
A4,Student A,FALSE,LB
6+
A5,Student A,FALSE,LB
7+
A6,NA,NA,NA
8+
A7,Student B,TRUE,MM
9+
A8,Student B,TRUE,MM
10+
A9,Student B,FALSE,MM
11+
A10,Student B,FALSE,MM
12+
A11,NA,NA,NA
13+
A12,NA,NA,NA
14+
B1,NA,NA,NA
15+
B2,Student C,TRUE,LB
16+
B3,Student C,TRUE,LB
17+
B4,Student C,FALSE,LB
18+
B5,Student C,FALSE,LB
19+
B6,NA,NA,NA
20+
B7,Student D,TRUE,MM
21+
B8,Student D,TRUE,MM
22+
B9,Student D,FALSE,MM
23+
B10,Student D,FALSE,MM
24+
B11,NA,NA,NA
25+
B12,NA,NA,NA
26+
C1,NA,NA,NA
27+
C2,Student E,TRUE,LB
28+
C3,Student E,TRUE,LB
29+
C4,Student E,FALSE,LB
30+
C5,Student E,FALSE,LB
31+
C6,NA,NA,NA
32+
C7,Student F,TRUE,MM
33+
C8,Student F,TRUE,MM
34+
C9,Student F,FALSE,MM
35+
C10,Student F,FALSE,MM
36+
C11,NA,NA,NA
37+
C12,NA,NA,NA
38+
D1,NA,NA,NA
39+
D2,Student G,TRUE,LB
40+
D3,Student G,TRUE,LB
41+
D4,Student G,FALSE,LB
42+
D5,Student G,FALSE,LB
43+
D6,NA,NA,NA
44+
D7,Student H,TRUE,MM
45+
D8,Student H,TRUE,MM
46+
D9,Student H,FALSE,MM
47+
D10,Student H,FALSE,MM
48+
D11,NA,NA,NA
49+
D12,NA,NA,NA
50+
E1,NA,NA,NA
51+
E2,Student I,TRUE,LB
52+
E3,Student I,TRUE,LB
53+
E4,Student I,FALSE,LB
54+
E5,Student I,FALSE,LB
55+
E6,NA,NA,NA
56+
E7,Student J,TRUE,MM
57+
E8,Student J,TRUE,MM
58+
E9,Student J,FALSE,MM
59+
E10,Student J,FALSE,MM
60+
E11,NA,NA,NA
61+
E12,NA,NA,NA
62+
F1,NA,NA,NA
63+
F2,Student K,TRUE,LB
64+
F3,Student K,TRUE,LB
65+
F4,Student K,FALSE,LB
66+
F5,Student K,FALSE,LB
67+
F6,NA,NA,NA
68+
F7,Student L,TRUE,MM
69+
F8,Student L,TRUE,MM
70+
F9,Student L,FALSE,MM
71+
F10,Student L,FALSE,MM
72+
F11,NA,NA,NA
73+
F12,NA,NA,NA
74+
G1,NA,NA,NA
75+
G2,Student M,TRUE,LB
76+
G3,Student M,TRUE,LB
77+
G4,Student M,FALSE,LB
78+
G5,Student M,FALSE,LB
79+
G6,NA,NA,NA
80+
G7,Student N,TRUE,MM
81+
G8,Student N,TRUE,MM
82+
G9,Student N,FALSE,MM
83+
G10,Student N,FALSE,MM
84+
G11,NA,NA,NA
85+
G12,NA,NA,NA
86+
H1,NA,NA,NA
87+
H2,Student O,TRUE,LB
88+
H3,Student O,TRUE,LB
89+
H4,Student O,FALSE,LB
90+
H5,Student O,FALSE,LB
91+
H6,NA,NA,NA
92+
H7,Student P,TRUE,MM
93+
H8,Student P,TRUE,MM
94+
H9,Student P,FALSE,MM
95+
H10,Student P,FALSE,MM
96+
H11,NA,NA,NA
97+
H12,NA,NA,NA

0 commit comments

Comments
 (0)