GitHub - 14zac2/HealthyWoodchuckMap: Scripts relating to the clustering and analysis of the healthy woodchuck liver map.

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Scripts relating to the clustering and analysis of the healthy woodchuck liver map.

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Name		Name	Last commit message	Last commit date
Latest commit History 94 Commits
figures		figures
woodchuck-spatial-v1		woodchuck-spatial-v1
woodchuck-spatial-v2		woodchuck-spatial-v2
WCK01_AAH20201022_F8-SC1.anno20210519.gff3.gz		WCK01_AAH20201022_F8-SC1.anno20210519.gff3.gz
WHV vs HBV scatterplots.Rmd		WHV vs HBV scatterplots.Rmd
addCellTypes.Rmd		addCellTypes.Rmd
addCellTypes.nb.html		addCellTypes.nb.html
clustering.R		clustering.R
countCellTypesPerWoodchuck.Rmd		countCellTypesPerWoodchuck.Rmd
countCellTypesPerWoodchuck.nb.html		countCellTypesPerWoodchuck.nb.html
countFilteredCells.Rmd		countFilteredCells.Rmd
countFilteredCells.nb.html		countFilteredCells.nb.html
downsample_PMAIO_unstim.Rmd		downsample_PMAIO_unstim.Rmd
downsample_PMAIO_unstim.nb.html		downsample_PMAIO_unstim.nb.html
dropletQC_plots.Rmd		dropletQC_plots.Rmd
dropletQC_plots.nb.html		dropletQC_plots.nb.html
exportUCSC.Rmd		exportUCSC.Rmd
exportUCSC.nb.html		exportUCSC.nb.html
figureGeneration.Rmd		figureGeneration.Rmd
figureGeneration.nb.html		figureGeneration.nb.html
findIntersectingMarkers.Rmd		findIntersectingMarkers.Rmd
findIntersectingMarkers.nb.html		findIntersectingMarkers.nb.html
healthy_sc.Rproj		healthy_sc.Rproj
mergeAllSamples.Rmd		mergeAllSamples.Rmd
mergeAllSamples.nb.html		mergeAllSamples.nb.html
mergeHealthy.R		mergeHealthy.R
mitoCutoffs.Rmd		mitoCutoffs.Rmd
mitoCutoffs.nb.html		mitoCutoffs.nb.html
pathwayAnalysis.Rmd		pathwayAnalysis.Rmd
pathwayAnalysis.nb.html		pathwayAnalysis.nb.html
prep_ucsc.Rmd		prep_ucsc.Rmd
prep_ucsc.nb.html		prep_ucsc.nb.html
reintegrateDiseased.Rmd		reintegrateDiseased.Rmd
reintegrateDiseased.nb.html		reintegrateDiseased.nb.html
scoreCellLineages.Rmd		scoreCellLineages.Rmd
scoreCellLineages.nb.html		scoreCellLineages.nb.html
spatial.R		spatial.R
spatialTranscriptomics.Rmd		spatialTranscriptomics.Rmd
spatialTranscriptomics.nb.html		spatialTranscriptomics.nb.html
stimulationExperiments.Rmd		stimulationExperiments.Rmd
stimulationExperiments.nb.html		stimulationExperiments.nb.html
stimulationExperiments_pmaio_unstim_downsampled_cca_kanchor5.html		stimulationExperiments_pmaio_unstim_downsampled_cca_kanchor5.html
stimulationExperiments_rpca_kanchor20.html		stimulationExperiments_rpca_kanchor20.html
stimulationExperiments_subclustering.Rmd		stimulationExperiments_subclustering.Rmd
stimulationExperiments_subclustering.nb.html		stimulationExperiments_subclustering.nb.html
subclustering.Rmd		subclustering.Rmd
subclustering.nb.html		subclustering.nb.html