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A selection of perl, python, bash, and R scripts used in general analyses

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309 Commits
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Annotations
 
 
Homoplasy
Homoplasy
 
 
LiteratureReview
LiteratureReview
 
 
NewZealand
NewZealand
 
 
Paratuberculosis
Paratuberculosis
 
 
PhylogeneticTree
PhylogeneticTree
 
 
ProcessingPipeline
ProcessingPipeline
 
 
RepublicOfIreland
RepublicOfIreland
 
 
Sequences
Sequences
 
 
SpoligotypeR
SpoligotypeR
 
 
Spoligotyping
Spoligotyping
 
 
SummerStudent
SummerStudent
 
 
TVR
TVR
 
 
TempoR
TempoR
 
 
WoodchesterPark
WoodchesterPark
 
 
.RData
.RData
 
 
.Rhistory
.Rhistory
 
 
ComparingConvexAndConcaveHulls_13-06-17.R
ComparingConvexAndConcaveHulls_13-06-17.R
 
 
ComparingPhylogenies_15-06-18.R
ComparingPhylogenies_15-06-18.R
 
 
ConvertHerdEastNorthingsToLatLongs_22-03-2018.R
ConvertHerdEastNorthingsToLatLongs_22-03-2018.R
 
 
ConvertPDFToPNG_25-06-19.sh
ConvertPDFToPNG_25-06-19.sh
 
 
DemonstrateMakingGiff_29-03-18.R
DemonstrateMakingGiff_29-03-18.R
 
 
ExamingSpatialClusteringInClades_Lili_19-11-18.R
ExamingSpatialClusteringInClades_Lili_19-11-18.R
 
 
ExaminingEggCounts_11-10-19.R
ExaminingEggCounts_11-10-19.R
 
 
FittingRandomForestModel_17-10-17.R
FittingRandomForestModel_17-10-17.R
 
 
GetConsensusFromClustalAlignment_28-09-17.R
GetConsensusFromClustalAlignment_28-09-17.R
 
 
HelpingTaherPlotTickSampling_16-10-19.R
HelpingTaherPlotTickSampling_16-10-19.R
 
 
HelpingYao_qPCRResults_30-09-19.R
HelpingYao_qPCRResults_30-09-19.R
 
 
LICENSE
LICENSE
 
 
MultithreadingInR_27-08-18.R
MultithreadingInR_27-08-18.R
 
 
OverlayTextFunctions_08-02-18.R
OverlayTextFunctions_08-02-18.R
 
 
Pathogen.cl.1.0.xlsx
Pathogen.cl.1.0.xlsx
 
 
PlotHerdSizeDistribution_14-06-18.R
PlotHerdSizeDistribution_14-06-18.R
 
 
PlotTwoHistograms.R
PlotTwoHistograms.R
 
 
PlottingPhylogeneticTreeAndEstimatingAncestralStates_14-03-18.R
PlottingPhylogeneticTreeAndEstimatingAncestralStates_14-03-18.R
 
 
README.md
README.md
 
 
RunRAXML_27-06-18.R
RunRAXML_27-06-18.R
 
 
SyncGitRepository_09-01-17.sh
SyncGitRepository_09-01-17.sh
 
 
TestingAddTextLabels_12-08-18.R
TestingAddTextLabels_12-08-18.R
 
 
ThinkingAboutNormalisation_06-12-17.R
ThinkingAboutNormalisation_06-12-17.R
 
 
TreeBuildingUsingVNTRAndSpoligotype_Assel_07-02-18.R
TreeBuildingUsingVNTRAndSpoligotype_Assel_07-02-18.R
 
 

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GeneralTools

A selection of perl, R, python, and shell scripts used in general analyses

This code is associated with the paper from Crispell et al., "Combining genomics and epidemiology to analyse bi-directional transmission of Mycobacterium bovis in a multi-host system". eLife, 2019. http://doi.org/10.7554/eLife.45833

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A selection of perl, python, bash, and R scripts used in general analyses

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  • HTML 73.6%
  • R 22.2%
  • Perl 1.9%
  • Python 1.2%
  • Shell 1.1%