Man pages for SingerLab/gac
Genetic Analysis of Cells

addCellsAdd cells to an existing cnr
addInfoAdds info to the chromInfo
addPhenoAdds additional phenotypes for a new trait
addQCaddQC
ampColampCol - ComplexHeatmap scale
binary.cnrbuild binary CNR from integer copy number data
binary.matbinary matrix
binary.Xbuild binary matrix from integer copy number data
buildCNRBuild a CNR bundle (Copy Number, -Rounded)
ccClustColccClustCol - ComplexHeatmap color scale
chromInfoChromosome coordinates and additional data of the bins
cluster_heterogeneitycluster heterogeneity across the sample
cluster_representationcluster representation
cnrcnr: copy number, rounded
consensusClusterCNRrun consensus clustering
copynumbersCopy number quantal matrix (copynumbers)
depmap_annotateannotate essential genes w/DepMap
DepScoresRead DepMap D2_combined file
distCNRcalculating cell-to-cell distances for clustering
dnadna: a cnr with bulk DNA like copy number data
doKSpectralRun Specral K to select optimum and maximum K from Consensus...
epseps : Spacing of floating point numbers
excludeCellsexclude cells from CNR bundle
expand2genesExpands the bins to genes
exportCNRexport CNR to flat text files
fgaColfgaCol - ComplexHeatmap Legend
fisher_treeimplementation of fisher_dist, hc, and tree
GACgac
gene.aggregatecombine genes w/equal frequency to be only once
gene.indexBin-to-gene index
genotype_vdjGenotype cells at the VDJ recombination sites
get_alt_frequenciesalteration frequency (both Amp + Del)
get_alt_frequenciesCNRestimate bin and gene alteration frequencies
get_amp_frequenciesamplification gene frequency
get_bin_frequenciesestimate bin alteration frequencies
get_cluster_profilesBuild a consensus copy number profile for each cluster or...
get_del_frequenciesdeletion frequency
get_gene_detailsPull gene details for a genomic region
get_gene_frequenciesestimate bin alteration frequencies
getSubclonesCNRimplementation of finding clones and subclones from SCclust
gisticGRGistic Genomic Ranges, get genes in gene.index that overlap...
gisticRegionsProcess GISTIC2 output // output only grTR read in gistic...
hclustCNRheirarchical clustering
HeatmapCNRHeatmapCNR
hg19_cytoBandHG19 cytoband file from UCSC genome browser
keepCellsexclude cells from CNR bundle
kSpectralkSpectral
legAmplegAmp - ComplexHeatmap Legend
legFGAlegFGA - ComplexHeatmap Legend
legLog2RlegSeg - ComplexHeatmap Legend
legPloidylegPloidy - ComplexHeatmap Legend
legSeglegSeg - ComplexHeatmap Legend
lookupCNLookup copy number data from bins
lowCollowCol - ComplexHeatmap color scale
mapdMedian absolute pairwise deviance (MAPD)
mark.genesMark genes
minimum.intersectMinimum tree.height at the intersect of one-cell and...
nbinsnumber of bins
ncellsnumber of cells in cnr
ngenesnumber of genes in gene.index
nphenonumber of phenotypes
oncoKB_annotateannotate gene index with oncoKB
optClustoptimizing clustering for single-cell copy number
parctanPeter Andrew's arctan transformation for visualizing copy...
phenoSingle-cell phenotype annotation
phyloCNRCalculating cell-to-cell distances, heirarchical clustering,...
phyloDDRCCalculating clone-to-clone distances, and estimating a...
ploginternal
ploidyColploidyCol - ComplexHeatmap Legend
plot_ccpplot consensus clustering
plotCLplot cluster optimization
plot_frequenciesplot genome-wide amplification and deletion frequencies
pull_gene_detailsPull gene details for a genomic region
qcQuality control annotation
rank_clonesrank clones
roundCNRrounded quantal matrix
scClustCNRimplementation of SCclust pipeline
segColsegCol - ComplexHeatmap color scale
setBrayClustersSet clusters using one-cell and multi-cell height...
setKccSet cluster membership for K clusters
sim_fisherCNRimplementation of SCclust sim_fisher_wrapper
sinkhornKnoppsinkhornKnopp
subsetCNRSubset a set of bins or genes from a CNR object
subset_on_binssubset based on bins
subset_on_chromsubset based on complete chromosomes
subset_on_coordinatessubset based on complete chromosomes
subset_on_genessubset based on genes
summaryCNRsummary of cnr bundle
symmetricSinkhornKnoppsymmetricSinkhornKnopp
ternary.cnrbuild ternary matrix from integer copy number data
use_clustersselect clusters to use based on a minimum number of cells
vdjBrayClustVDJ cells bray clustering
vdjHeatmapHeatmap of cells with VDJ recombination
vdjPlotClustplot VDJ clustering
SingerLab/gac documentation built on July 22, 2021, 3:27 a.m.