Man pages for jlaffy/scalop
Single Cell Analysis Operations

add_to_dataframeJoin a dataframe and a named vector
aggr_gene_exprlog-Average expression of genes across all cells
annomapOne-bar annotation ggplot
as_bulkConvert sc-matrix to simulated bulk
as_bulk_samplesConvert sc-matrix to simulated bulk samples matrix
as_four_state_gbmConvert 6-state to 4-state GBM scores
assign_bulk_statesAssign Samples to States by High- and Low -frequency of their...
baseScoresBasic Scoring of Matrix by Gene sigs
binGenerate Equally-Sized Bins
binmatchControl Signatures From Expression Bins
bootstrapped_state_fractionsBootstrapped State Fractions
bootstrap_summarySummary Statistics for Bootstrapped State Fractions
cluster.methodsagglomeration method in hierarchical clustering agglomeration...
colcenterCenter a matrix column-wise
coldetectedNumber of non-zero values per column
combine_group2_deaAggregate 'scalop::dea' output for one group against many in...
complyApply a Function to All Pairs of Elements in 'x' or Between...
cor.methodsCorrelation method method for computing correlation...
cpmConvert Counts to Counts-Per-Million (CPM)
deaDifferential Expression Analysis
dims<dim> for many matrices
discrete_coloursThe 297 discrete colours available across different...
dist.methodsdistance metric method for computing distances from a matrix...
doubletCellsIdentify potential doublet cells
enricherFUNCTION_TITLE
ensembl2symbolensembl2symbol
expr_housekeepingExpression level of Housekeeping Genes
extract_sample_namesExtract Sample Names
extract_substringFind and Extract substrings
filter_signaturesFilter Out Lowly-Correlated Genes from Signature(s)
filter_sigsFilter genes in sigs according to reference
fitBimodalFit a Bimodal Gaussian Distribution
flipFlip the (nested) elements of a character vector (or list)...
foldchangefold changes
frac_mitoFraction of a Cell's Expression Level Coming From...
futuramafuturama, 12 Discrete Colours
GeneInfoGet Genomic Information
genericModelFUNCTION_TITLE
getGRChGet hg19 or hg38 information from biomaRt
get_signaturesFUNCTION_TITLE
get_snn_graph_clustersFUNCTION_TITLE
ggDensityFUNCTION_TITLE
ggmapgmap wrapper
ggoutliersPlot model and Outliers
ggpubrggpubr, 3 Discrete Colours
ggvolcanoFUNCTION_TITLE
gmapPlot A Heatmap with ggplot2
grombineCombine ggplot grobs or plots
grouped_reorderGrouped Reorder and Ungroup
grouped_rowcenterCenter matrix rows by subsets of columns
hcaHierarchical clustering analysis
headlLeft-hand head a matrix or dataframe
headrRight-hand head a matrix or dataframe
hierarchyCell state hierarchy coordinates
hms_spanSubtract POSIXt Class Objects in HH:MM:SS Format
jaccardCompute Jaccard Similarities between Pairs of Character...
jacFiltFilter List By Jaccard
jacmapConvert a list to a jaccard matrix and plot with...
ldcastTurn a list into a dataframe
logcpmConvert CPM to logCPM
logRowMeansRow Means of Log2 data
markerScoresScore a Matrix with Marker Gene Sets Of Normal Cell Types
Markers_NormalMarker gene sets of Normal Cell Types and Pan-Cancer Programs
mat01Character List to Binary (membership) Matrix
maxcol_strictStrict Column Assign
metaprogramsCompute Metaprograms
ncols<ncol> for many matrices
NormalBrainSignatures98 Signatures for Normal Brain Cell Types
NormalBrainSignatures298 Signatures for Normal Brain Cell Types
NormalBrainSignatures3178 Signatures for Normal Brain Cell Types
NormalSignatures205 Signatures for Normal Cell Types
nrows<nrow> for many matrices
nSigGenesFUNCTION_TITLE
ohmyqcQuality control statistics for single cell RNA seq data
ohmySNNclustersSNN Graph-Based Clustering
ohmytsneA plot-friendly output for the Barnes-Hut implementation of...
outliersFUNCTION_TITLE
pal19pal19, 19 Pretty Discrete Colours
pal28pal28, 28 Pretty Discrete Colours
palG34RpalG34R, a palette of reds and blues for cases within two...
pcaFUNCTION_TITLE
pipePipe operator
plot_hierarchyPlot State Hierarchy (Quadrant plot)
programsFind cell clusters and retrieve significant expresion...
range_rowmeansRange of the rowMeans of a matrix
rowcenterCenter a matrix row-wise
rowdetectedNumber of non-zero values per row
sample_strictAssign Rows and Sample
Sapplysapply wrapper
scdatascRNA-seq data from a patient with Glioblastoma
scoreScore matrix columns for groups of rows
setColNamesSet the colnames in an object
setRowNamesSet the rownames in an object
sigScoresScore a Matrix by Gene sigs (Signatures)
simpsonssimpsons, 16 Discrete Colours
split_by_sample_namesSplit Character Vector of Cell IDs by Sample Names
split_by_substringSplit Character Vector by Pattern Matching
state_fractionsState Fractions (by group)
state_high_genesGenes Associated with High Frequency of a Cellular State
taillLeft-hand tail a matrix or dataframe
tailrRight-hand tail a matrix or dataframe
tpmConvert logTPM to TPM
unique_sample_namesGet unique sample names
UnlistUnlist, keeping original list or element names
unlogcpmConvert logCPM to CPM
unlogtpmConvert TPM to logTPM
unpack-assignDestructuring assignment
unpack-assign-backDestructuring assignment
vannomapOne-bar annotation ggplot
wilcoxtestwilcoxon-tests
jlaffy/scalop documentation built on June 16, 2020, 3:46 p.m.