rebear217/PhageMFiles-v1.0.zip
rebear217-PhageMFiles-a4c0ccc
.gitattributes
66 Bytes
.gitignore
10 Bytes
data
11a_RYTO.xlsx
145.8 kB
13a_RYTO.xlsx
26.1 kB
13b_RYTO.xlsx
145.2 kB
14a_RYTO.xlsx
186.3 kB
17a_RYTO.xlsx
188.7 kB
18a_RYTO.xlsx
190.2 kB
19a_RYTO.xlsx
70.7 kB
21b_RYTO.xlsx
145.1 kB
22a_RYTO.xlsx
145.7 kB
23b_RYTO.xlsx
145.1 kB
26a_RYTO.xlsx
151.8 kB
27a_RYTO.xlsx
145.4 kB
28b_RYTO.xlsx
190.0 kB
29a_RYTO.xlsx
146.2 kB
2b_RYTO.xlsx
144.9 kB
30a_RYTO.xlsx
145.5 kB
41a_RYTO.xlsx
144.8 kB
47a_RYTO.xlsx
151.6 kB
4a_RYTO.xlsx
145.3 kB
50b_RYTO.xlsx
146.6 kB
51a_RYTO.xlsx
145.9 kB
51b_RYTO.xlsx
145.1 kB
56a_RYTO.xlsx
151.6 kB
57b_RYTO.xlsx
26.5 kB
59a_RYTO.xlsx
146.7 kB
60a_RYTO.xlsx
25.6 kB
61a_RYTO.xlsx
25.6 kB
61b_RYTO.xlsx
146.1 kB
62b_RYTO.xlsx
25.4 kB
66a_RYTO.xlsx
25.6 kB
68a_RYTO.xlsx
26.0 kB
69a_RYTO.xlsx
146.8 kB
70a_RYTO.xlsx
146.2 kB
70b_RYTO.xlsx
147.0 kB
71a_RYTO.xlsx
145.6 kB
71b_RYTO.xlsx
25.6 kB
7a_RYTO.xlsx
151.2 kB
8a_RYTO.xlsx
146.3 kB
94a_RYTO.xlsx
26.0 kB
95a_RYTO.xlsx
191.1 kB
96b_RYTO.xlsx
25.4 kB
97b_RYTO.xlsx
71.0 kB
98a_RYTO.xlsx
71.0 kB
99a_RYTO.xlsx
25.8 kB
9a_RYTO.xlsx
146.2 kB
Fitness data for Rob 8_31_15.xlsx
52.3 kB
RKandLagData.mat
140.7 kB
RPM clearing data for Beardmore 2022.xlsx
8.0 kB
allCarbonData.mat
245.4 kB
allData.mat
389.3 kB
anc_RYTO.xlsx
174.4 kB
ancestor_RYTO.xlsx
25.6 kB
derivedRKYieldData.xlsx
234.9 kB
derivedRelativeTraitData.xlsx
8.7 kB
phi-secondTry-large.mat
11.1 kB
relativeFitnessData.mat
2.7 kB
dataRepo
derivedData
RKYield
derivedRKYieldData.xlsx
210.0 kB
WTrelativeTraits
derivedRelativeTraitData.xlsx
7.9 kB
infectionMatrix
matrixData.xlsx
68.7 kB
phageCalibration
RPM clearing data for Beardmore 2022.xlsx
8.0 kB
rawData
OD-RYTO-runs
11a_RYTO.xlsx
145.8 kB
13a_RYTO.xlsx
26.1 kB
13b_RYTO.xlsx
145.2 kB
14a_RYTO.xlsx
186.3 kB
17a_RYTO.xlsx
188.7 kB
18a_RYTO.xlsx
190.2 kB
19a_RYTO.xlsx
70.7 kB
21b_RYTO.xlsx
145.1 kB
22a_RYTO.xlsx
145.7 kB
23b_RYTO.xlsx
145.1 kB
26a_RYTO.xlsx
151.8 kB
27a_RYTO.xlsx
145.4 kB
28b_RYTO.xlsx
190.0 kB
29a_RYTO.xlsx
146.2 kB
2b_RYTO.xlsx
144.9 kB
30a_RYTO.xlsx
145.5 kB
41a_RYTO.xlsx
144.8 kB
47a_RYTO.xlsx
151.6 kB
4a_RYTO.xlsx
145.3 kB
50b_RYTO.xlsx
146.6 kB
51a_RYTO.xlsx
145.9 kB
51b_RYTO.xlsx
145.1 kB
56a_RYTO.xlsx
151.6 kB
57b_RYTO.xlsx
26.5 kB
59a_RYTO.xlsx
146.7 kB
60a_RYTO.xlsx
25.6 kB
61a_RYTO.xlsx
25.6 kB
61b_RYTO.xlsx
146.1 kB
62b_RYTO.xlsx
25.4 kB
66a_RYTO.xlsx
25.6 kB
68a_RYTO.xlsx
26.0 kB
69a_RYTO.xlsx
146.8 kB
70a_RYTO.xlsx
146.2 kB
70b_RYTO.xlsx
147.0 kB
71a_RYTO.xlsx
145.6 kB
71b_RYTO.xlsx
25.6 kB
7a_RYTO.xlsx
151.2 kB
8a_RYTO.xlsx
146.3 kB
94a_RYTO.xlsx
26.0 kB
95a_RYTO.xlsx
191.1 kB
96b_RYTO.xlsx
25.4 kB
97b_RYTO.xlsx
71.0 kB
98a_RYTO.xlsx
71.0 kB
99a_RYTO.xlsx
25.8 kB
9a_RYTO.xlsx
146.2 kB
anc_RYTO.xlsx
174.4 kB
ancestor_RYTO.xlsx
25.6 kB
phageCalibration
Lab 2022-02-18_09h10m46s.tif
1.3 MB
Lab 2022-02-18_09h10m46s_inverted.tif
1.3 MB
Meyer clearing data for Beardmore 2022.csv
354 Bytes
phageImages
11a.jpg
15.3 kB
13a.jpg
12.9 kB
13b.jpg
13.4 kB
14a.jpg
15.0 kB
17a.jpg
13.7 kB
18a.jpg
18.1 kB
19a.jpg
14.5 kB
1a.jpg
14.4 kB
20b.jpg
12.8 kB
21a.jpg
13.4 kB
21b.jpg
14.2 kB
22a.jpg
13.4 kB
23b.jpg
13.6 kB
26a.jpg
11.5 kB
27a.jpg
13.6 kB
28a.jpg
11.7 kB
28b.jpg
11.2 kB
29a.jpg
12.0 kB
2b.jpg
12.7 kB
30a.jpg
14.8 kB
41a.jpg
13.9 kB
47a.jpg
15.7 kB
4a.jpg
15.7 kB
50b.jpg
13.9 kB
51a.jpg
12.2 kB
51b.jpg
14.9 kB
52a.jpg
13.8 kB
56a.jpg
12.2 kB
57b.jpg
13.7 kB
59a.jpg
13.2 kB
606 final plate.jpg
16.6 kB
606 first plate.jpg
26.4 kB
60a.jpg
16.4 kB
61a.jpg
14.6 kB
61b.jpg
13.7 kB
62b.jpg
16.9 kB
65b.jpg
13.9 kB
66a.jpg
16.8 kB
67a.jpg
13.7 kB
68a.jpg
13.9 kB
69a.jpg
13.5 kB
70a.jpg
13.5 kB
70b.jpg
13.5 kB
71a.jpg
14.7 kB
71b.jpg
13.1 kB
7a.jpg
16.1 kB
8a.jpg
15.8 kB
94a.jpg
12.6 kB
95a.jpg
12.0 kB
96a.jpg
12.6 kB
96b.jpg
14.9 kB
97b.jpg
16.3 kB
98a.jpg
12.1 kB
99a.jpg
13.9 kB
9a.jpg
13.3 kB
proteinCoords
11a coordinates.xls
1.5 MB
13a coordinates.xls
678.9 kB
13b coordinates.xls
1.4 MB
14a coordinates.xls
1.5 MB
17a coordinates.xls
1.5 MB
18a coordinates.xls
1.5 MB
19a coordinates.xls
683.5 kB
1a coordinates.xls
1.5 MB
20b coordinates.xls
286.2 kB
21b coordinates.xls
1.5 MB
22a coordinates.xls
1.5 MB
23b coordinates.xls
1.5 MB
26a coordinates.xls
1.1 MB
27a coordinates.xls
498.7 kB
28a coordinates.xls
554.0 kB
28b coordinates.xls
554.0 kB
29a coordinates.xls
1.5 MB
2b coordinates.xls
1.5 MB
30a coordinates.xls
1.5 MB
41a coordinates.xls
1.5 MB
47a coordinates.xls
1.1 MB
4a coordinates.xls
1.5 MB
50b coordinates.xls
1.5 MB
51a coordinates.xls
1.5 MB
51b coordinates.xls
1.5 MB
52a coordinates.xls
1.5 MB
56a coordinates.xls
1.4 MB
57b coordinates.xls
1.5 MB
59a coordinates.xls
1.5 MB
60a coordinates.xls
1.5 MB
61a coordinates.xls
1.5 MB
61b coordinates.xls
1.5 MB
62b coordinates.xls
1.4 MB
65b coordinates.xls
1.1 MB
66a coordinates.xls
1.1 MB
67a coordinates.xls
89.6 kB
68a coordinates.xls
1.1 MB
69a coordinates.xls
1.5 MB
70a coordinates.xls
1.1 MB
70b coordinates.xls
1.4 MB
71a coordinates.xls
1.5 MB
71b coordinates.xls
1.5 MB
7a coordinates.xls
1.5 MB
8a coordinates.xls
1.5 MB
94a coordinates.xls
1.4 MB
95a coordinates.xls
1.1 MB
96a coordinates.xls
566.3 kB
96b coordinates.xls
1.5 MB
97b coordinates.xls
1.5 MB
98a coordinates.xls
1.4 MB
99a coordinates.xls
1.5 MB
9a coordinates.xls
1.5 MB
w+ coordinates.xls
1.5 MB
relativeFitnesses
Fitnesses.xlsx
52.3 kB
dataTasks.m
521 Bytes
figureTasks.m
4.1 kB
figures
2btoWTmatch2.pdf
49.1 kB
56atoWTmatch1.pdf
177.3 kB
56atoWTmatch2.pdf
49.6 kB
AreaPFU.pdf
19.8 kB
GrowthRatePlotFor26a.pdf
335.0 kB
GrowthRatePlotFor56a.pdf
318.7 kB
GrowthRatePlotForWT.pdf
282.5 kB
HotSpotClusters@0.01-allMutations.pdf
57.9 kB
HotSpotClusters@0.01-completeResistanceMutants.pdf
39.4 kB
YieldAndRateCorrelation.pdf
307.3 kB
YieldAndRateCorrelationAllData.pdf
284.2 kB
allHotspotsLamBMovers.pdf
1.3 MB
allRYTOplots.pdf
1.9 MB
exampleMatching.pdf
30.5 kB
exampleMatchingPoints.pdf
14.6 kB
findResistantGrowthRateTOsAndTUs.pdf
18.9 kB
findResistantKmTOsAndTUs.pdf
18.4 kB
findResistantRmaxTOsAndTUs.pdf
18.9 kB
infectionMatrix-imageSc.pdf
60.7 kB
modularityPhiGraph.pdf
84.6 kB
modularityPhiMatrix.pdf
33.6 kB
phiLinearRegressions.pdf
596.5 kB
plotOneLagExample19a.pdf
22.4 kB
plotOneLagExamplewt.pdf
21.3 kB
relativeFitness.pdf
29.0 kB
unused
LagTOplotFor26a.pdf
234.5 kB
LagTOplotFor56a.pdf
235.6 kB
LagTOplotForWT.pdf
240.3 kB
RYTOplotFor26a.pdf
254.7 kB
RYTOplotFor56a.pdf
275.4 kB
RYTOplotForWT.pdf
293.6 kB
RY_RYTOplotFor26a.pdf
16.6 kB
RY_RYTOplotFor56a.pdf
25.3 kB
RY_RYTOplotForWT.pdf
27.6 kB
src
MeanShiftCluster.m
6.0 kB
allHotspotsLamBMovers.m
792 Bytes
analysePFUs.m
3.0 kB
distanceMatrix3d.m
374 Bytes
generateAllRKandLagData.m
332 Bytes
generateDerivedRKYieldXLSfile.m
1.4 kB
generateDerivedRRmaxKmXLSfile.m
156 Bytes
getFirstNonlinearPoint2.m
1.1 kB
getLocationLabels.m
100 Bytes
getRKdataFromLabel.m
3.4 kB
importAllTheData.m
2.1 kB
importData.m
607 Bytes
logisticFitToOD.m
3.5 kB
logisticFitToODfromLabel.m
1.5 kB
matchPoints3d.m
466 Bytes
meanPairwiseDistance.m
253 Bytes
myFFTSmooth.m
287 Bytes
mySmooth.m
184 Bytes
nestedAnalysis.m
1.1 kB
phiLinearRegressions.m
2.3 kB
plotAProtein.m
341 Bytes
plotAProtein1.m
200 Bytes
plotAProtein2.m
979 Bytes
plotAProteinColourVector.m
854 Bytes
plotAllLamBChanges.m
2.0 kB
plotAllRYTOs.m
1.2 kB
plotGrowthRatesFor.m
1.4 kB
plotHotSpotClusters.m
4.2 kB
plotInteractionMatrix.m
2.9 kB
plotJustRYTOfromLabel_FAST.m
12.6 kB
plotLamBDifferenceFromWt.m
3.8 kB
plotMutantDistancesOnLamB.m
1.7 kB
plotOneLagExample.m
1.5 kB
plotRYTOResistanceOutliers.m
19.4 kB
plotRYTOfromLabel_FAST.m
11.2 kB
plotRelFitness.m
3.1 kB
plotResistanceVersusTraitData_FAST.m
9.7 kB
plotSeveralLagExamples.m
1.9 kB
rectangularMatching.m
6.3 kB
rectangularMatchingLabels.m
1.3 kB
sphereTest
distanceMatrix3d.m
374 Bytes
matchPoints3d.m
466 Bytes
rectangularMatching.m
6.3 kB
sphereTest.m
1.4 kB
totalEuclidean.m
119 Bytes
worstMatches.m
192 Bytes
totalEuclidean.m
119 Bytes
worstMatches.m
192 Bytes
validVariables.m
1.1 kB