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A
ADT() (in module cellhub.pipeline_fetch_cells)
adt_plot_norm() (in module cellhub.pipeline_adt_norm)
adtdepth() (in module cellhub.pipeline_adt_norm)
adtdepthAPI() (in module cellhub.pipeline_adt_norm)
ambient_rna_compare() (in module cellhub.pipeline_ambient_rna)
ambient_rna_per_input() (in module cellhub.pipeline_ambient_rna)
anndata_from_h5() (in module cellhub.tasks.cellbender)
api (class in cellhub.tasks.api)
B
bcr() (in module cellhub.pipeline_cellranger)
C
cellbender() (in module cellhub.pipeline_cellbender)
cellhub.pipeline_adt_norm
module
cellhub.pipeline_ambient_rna
module
cellhub.pipeline_annotation
module
cellhub.pipeline_cell_qc
module
cellhub.pipeline_cellbender
module
cellhub.pipeline_celldb
module
cellhub.pipeline_cellranger
module
cellhub.pipeline_cluster
module
cellhub.pipeline_dehash
module
cellhub.pipeline_emptydrops
module
cellhub.pipeline_fetch_cells
module
cellhub.pipeline_singleR
module
cellhub.pipeline_velocyto
module
cellhub.tasks.api
module
cellhub.tasks.cellbender
module
cellhub.tasks.parameters
module
cellhub.tasks.profile
module
cellhub.tasks.setup
module
cellxgene() (in module cellhub.pipeline_cluster)
checkInputs() (in module cellhub.pipeline_velocyto)
clr_norm() (in module cellhub.pipeline_adt_norm)
clrAPI() (in module cellhub.pipeline_adt_norm)
cluster() (in module cellhub.pipeline_cluster)
clusterStats() (in module cellhub.pipeline_cluster)
clustree() (in module cellhub.pipeline_cluster)
compareClusters() (in module cellhub.pipeline_cluster)
concatenate() (in module cellhub.pipeline_singleR)
connect() (in module cellhub.pipeline_celldb)
count() (in module cellhub.pipeline_cellranger)
D
define_dataset() (cellhub.tasks.api.api method)
demuxEM() (in module cellhub.pipeline_dehash)
demuxemAPI() (in module cellhub.pipeline_dehash)
dePlots() (in module cellhub.pipeline_cluster)
dict_from_h5() (in module cellhub.tasks.cellbender)
dsb_norm() (in module cellhub.pipeline_adt_norm)
dsbAPI() (in module cellhub.pipeline_adt_norm)
E
emptyDrops() (in module cellhub.pipeline_emptydrops)
ensemblAPI() (in module cellhub.pipeline_annotation)
export() (in module cellhub.pipeline_cluster)
F
fetchCells() (in module cellhub.pipeline_fetch_cells)
fetchEnsembl() (in module cellhub.pipeline_annotation)
fetchKegg() (in module cellhub.pipeline_annotation)
final() (in module cellhub.pipeline_celldb)
findMarkers() (in module cellhub.pipeline_cluster)
full() (in module cellhub.pipeline_adt_norm)
(in module cellhub.pipeline_ambient_rna)
(in module cellhub.pipeline_cell_qc)
(in module cellhub.pipeline_cellbender)
(in module cellhub.pipeline_cellranger)
(in module cellhub.pipeline_emptydrops)
(in module cellhub.pipeline_velocyto)
G
genClusterJobs() (in module cellhub.pipeline_velocyto)
genesetAnalysis() (in module cellhub.pipeline_cluster)
genesets() (in module cellhub.pipeline_cluster)
genSingleRjobs() (in module cellhub.pipeline_singleR)
get_parameter_file() (in module cellhub.tasks.parameters)
GEX() (in module cellhub.pipeline_fetch_cells)
gexdepth() (in module cellhub.pipeline_adt_norm)
gexdepthAPI() (in module cellhub.pipeline_adt_norm)
gmmAPI() (in module cellhub.pipeline_dehash)
gmmDemux() (in module cellhub.pipeline_dehash)
H
h5API() (in module cellhub.pipeline_cellbender)
(in module cellhub.pipeline_cellranger)
hashCountCSV() (in module cellhub.pipeline_dehash)
I
indir (cellhub.tasks.setup.setup attribute)
inname (cellhub.tasks.setup.setup attribute)
is_tool() (in module cellhub.tasks.profile)
J
job_memory (cellhub.tasks.setup.setup attribute)
job_threads (cellhub.tasks.setup.setup attribute)
K
keggAPI() (in module cellhub.pipeline_annotation)
L
latexVars() (in module cellhub.pipeline_cluster)
load_demuxEM() (in module cellhub.pipeline_celldb)
load_gex_qcmetrics() (in module cellhub.pipeline_celldb)
load_gex_scrublet() (in module cellhub.pipeline_celldb)
load_gmm_demux() (in module cellhub.pipeline_celldb)
load_samples() (in module cellhub.pipeline_celldb)
load_singleR() (in module cellhub.pipeline_celldb)
load_souporcell() (in module cellhub.pipeline_celldb)
log_file (cellhub.tasks.setup.setup attribute)
loom() (in module cellhub.pipeline_cluster)
M
markerPlots() (in module cellhub.pipeline_cluster)
markerReport() (in module cellhub.pipeline_cluster)
markerReportSource() (in module cellhub.pipeline_cluster)
markers() (in module cellhub.pipeline_cluster)
meanReads() (in module cellhub.pipeline_emptydrops)
median_norm() (in module cellhub.pipeline_adt_norm)
medianAPI() (in module cellhub.pipeline_adt_norm)
mergeBCR() (in module cellhub.pipeline_cellranger)
mergeTCR() (in module cellhub.pipeline_cellranger)
metadata() (in module cellhub.pipeline_cluster)
module
cellhub.pipeline_adt_norm
cellhub.pipeline_ambient_rna
cellhub.pipeline_annotation
cellhub.pipeline_cell_qc
cellhub.pipeline_cellbender
cellhub.pipeline_celldb
cellhub.pipeline_cellranger
cellhub.pipeline_cluster
cellhub.pipeline_dehash
cellhub.pipeline_emptydrops
cellhub.pipeline_fetch_cells
cellhub.pipeline_singleR
cellhub.pipeline_velocyto
cellhub.tasks.api
cellhub.tasks.cellbender
cellhub.tasks.parameters
cellhub.tasks.profile
cellhub.tasks.setup
mtx() (in module cellhub.pipeline_cellbender)
mtxAPI() (in module cellhub.pipeline_cellbender)
(in module cellhub.pipeline_cellranger)
N
neighbourGraph() (in module cellhub.pipeline_cluster)
O
outdir (cellhub.tasks.setup.setup attribute)
outname (cellhub.tasks.setup.setup attribute)
P
paga() (in module cellhub.pipeline_cluster)
parse_mem() (cellhub.tasks.setup.setup method)
parseDemuxEM() (in module cellhub.pipeline_dehash)
parseGMTs() (in module cellhub.pipeline_cluster)
plot() (in module cellhub.pipeline_adt_norm)
(in module cellhub.pipeline_ambient_rna)
(in module cellhub.pipeline_cell_qc)
plotGroupNumbers() (in module cellhub.pipeline_cluster)
plotMarkerNumbers() (in module cellhub.pipeline_cluster)
plotRdimsClusters() (in module cellhub.pipeline_cluster)
plotRdimsFactors() (in module cellhub.pipeline_cluster)
plotRdimsSingleR() (in module cellhub.pipeline_cluster)
plots() (in module cellhub.pipeline_cluster)
plotSingleR() (in module cellhub.pipeline_cluster)
preflight() (in module cellhub.pipeline_cluster)
Q
qcmetrics() (in module cellhub.pipeline_cell_qc)
qcmetricsAPI() (in module cellhub.pipeline_cell_qc)
R
register_dataset() (cellhub.tasks.api.api method)
registerBCR() (in module cellhub.pipeline_cellranger)
registerMergedBCR() (in module cellhub.pipeline_cellranger)
registerMergedTCR() (in module cellhub.pipeline_cellranger)
registerTCR() (in module cellhub.pipeline_cellranger)
report() (in module cellhub.pipeline_cluster)
reset_endpoint() (cellhub.tasks.api.api method)
resources (cellhub.tasks.setup.setup attribute)
runVelocyto() (in module cellhub.pipeline_velocyto)
S
scanpyCluster() (in module cellhub.pipeline_cluster)
scrublet() (in module cellhub.pipeline_cell_qc)
scrubletAPI() (in module cellhub.pipeline_cell_qc)
set_resources() (cellhub.tasks.setup.setup method)
setup (class in cellhub.tasks.setup)
show() (cellhub.tasks.api.api method)
singleR() (in module cellhub.pipeline_singleR)
singleRAPI() (in module cellhub.pipeline_singleR)
sortBam() (in module cellhub.pipeline_velocyto)
summariseGenesetAnalysis() (in module cellhub.pipeline_cluster)
summariseMarkers() (in module cellhub.pipeline_cluster)
summariseSingleR() (in module cellhub.pipeline_cluster)
summary() (in module cellhub.pipeline_singleR)
summaryReport() (in module cellhub.pipeline_cluster)
summaryReportSource() (in module cellhub.pipeline_cluster)
T
taskSummary() (in module cellhub.pipeline_cluster)
tcr() (in module cellhub.pipeline_cellranger)
topMarkerHeatmap() (in module cellhub.pipeline_cluster)
U
UMAP() (in module cellhub.pipeline_cluster)
useCounts() (in module cellhub.pipeline_cellbender)
(in module cellhub.pipeline_cellranger)
W
write_config_files() (in module cellhub.tasks.parameters)
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