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B
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C
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D
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E
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F
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G
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H
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I
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
B
bamOptions() (in module sincei.ParserCommon)
base_measure() (sincei.ExponentialFamily.Bernoulli method)
(sincei.ExponentialFamily.Beta method)
(sincei.ExponentialFamily.ExponentialFamily method)
(sincei.ExponentialFamily.Gaussian method)
(sincei.ExponentialFamily.LogNormal method)
(sincei.ExponentialFamily.Poisson method)
Bernoulli (class in sincei.ExponentialFamily)
Beta (class in sincei.ExponentialFamily)
C
CenterFragment (class in sincei.scBulkCoverage)
checkAlignedFraction() (in module sincei.Utilities)
checkBAMtag() (in module sincei.Utilities)
checkGCcontent() (in module sincei.Utilities)
checkMotifs() (in module sincei.Utilities)
colorPicker() (in module sincei.Utilities)
convertBED() (in module sincei.scBAMops)
count_occurrences() (in module sincei.scFilterBarcodes)
count_reads_in_region() (sincei.ReadCounter.CountReadsPerBin method)
countReadsInRegions_wrapper() (in module sincei.ReadCounter)
CountReadsPerBin (class in sincei.ReadCounter)
D
distribution() (sincei.ExponentialFamily.ExponentialFamily method)
E
estimateSizeFactors() (in module sincei.ReadCounter)
exponential_term() (sincei.ExponentialFamily.Beta method)
(sincei.ExponentialFamily.ExponentialFamily method)
(sincei.ExponentialFamily.Gamma method)
(sincei.ExponentialFamily.LogNormal method)
ExponentialFamily (class in sincei.ExponentialFamily)
F
fftplot() (in module sincei.FragmentFFT)
ffttable() (in module sincei.FragmentFFT)
filter_adata() (in module sincei.scCountQC)
filterOptions() (in module sincei.ParserCommon)
filterStrand() (sincei.scBulkCoverage.OffsetFragment method)
filterWorker() (in module sincei.scBAMops)
fit() (sincei.GLMPCA.GLMPCA method)
fragment_distribution() (in module sincei.FragmentFFT)
G
Gamma (class in sincei.ExponentialFamily)
Gaussian (class in sincei.ExponentialFamily)
genomicRegion() (in module sincei.ParserCommon)
get_args() (in module sincei.scBAMops)
(in module sincei.scBulkCoverage)
(in module sincei.scClusterCells)
(in module sincei.scCombineCounts)
(in module sincei.scCountQC)
(in module sincei.scCountReads)
(in module sincei.scFilterBarcodes)
(in module sincei.scJSD)
get_bins_by_gene() (in module sincei.RegionQuery)
get_cell_topic() (sincei.TopicModels.TOPICMODEL method)
get_chunk_length() (sincei.ReadCounter.CountReadsPerBin method)
get_coverage_of_region() (sincei.ReadCounter.CountReadsPerBin method)
get_default() (in module sincei.ParserCommon)
get_fragment_from_read() (sincei.ReadCounter.CountReadsPerBin method)
(sincei.scBulkCoverage.CenterFragment method)
(sincei.scBulkCoverage.OffsetFragment method)
get_fragment_from_read_list() (sincei.scBulkCoverage.OffsetFragment method)
get_gtf_adata_olaps() (in module sincei.RegionQuery)
getDupFilterTuple() (in module sincei.Utilities)
getFiltered_worker() (in module sincei.scFilterBarcodes)
(in module sincei.scFilterStats)
getRead() (sincei.ReadCounter.Tester method)
getReadLength() (sincei.ReadCounter.CountReadsPerBin method)
getSmoothRange() (sincei.ReadCounter.CountReadsPerBin method)
getStats_worker() (in module sincei.GetStats)
gini() (in module sincei.Utilities)
GLMPCA (class in sincei.GLMPCA)
H
ham_dist() (in module sincei.scFilterBarcodes)
I
initialize_family_parameters() (sincei.ExponentialFamily.Beta method)
(sincei.ExponentialFamily.ExponentialFamily method)
(sincei.ExponentialFamily.Gamma method)
(sincei.ExponentialFamily.LogNormal method)
inputOutputOptions() (in module sincei.ParserCommon)
invert_g() (sincei.ExponentialFamily.Bernoulli method)
(sincei.ExponentialFamily.Beta method)
(sincei.ExponentialFamily.ExponentialFamily method)
(sincei.ExponentialFamily.Gamma method)
(sincei.ExponentialFamily.Gaussian method)
(sincei.ExponentialFamily.LogNormal method)
(sincei.ExponentialFamily.Poisson method)
(sincei.ExponentialFamily.SigmoidBeta method)
is_proper_pair() (sincei.ReadCounter.CountReadsPerBin static method)
L
load_family_params_to_gpu() (sincei.ExponentialFamily.ExponentialFamily method)
log_distribution() (sincei.ExponentialFamily.ExponentialFamily method)
(sincei.ExponentialFamily.Poisson method)
log_likelihood() (sincei.ExponentialFamily.Bernoulli method)
(sincei.ExponentialFamily.ExponentialFamily method)
log_partition() (sincei.ExponentialFamily.Bernoulli method)
(sincei.ExponentialFamily.Beta method)
(sincei.ExponentialFamily.ExponentialFamily method)
(sincei.ExponentialFamily.Gamma method)
(sincei.ExponentialFamily.Gaussian method)
(sincei.ExponentialFamily.LogNormal method)
(sincei.ExponentialFamily.Poisson method)
LogNormal (class in sincei.ExponentialFamily)
M
main() (in module sincei.scBAMops)
(in module sincei.scBulkCoverage)
(in module sincei.scClusterCells)
(in module sincei.scCombineCounts)
(in module sincei.scCountQC)
(in module sincei.scCountReads)
(in module sincei.scFilterBarcodes)
(in module sincei.scFilterStats)
(in module sincei.scJSD)
(in module sincei.sincei)
module
sincei
sincei.ExponentialFamily
sincei.FragmentFFT
sincei.GetStats
sincei.GLMPCA
sincei.multimodalClustering
sincei.ParserCommon
sincei.ReadCounter
sincei.RegionQuery
sincei.scBAMops
sincei.scBulkCoverage
sincei.scClusterCells
sincei.scCombineCounts
sincei.scCountQC
sincei.scCountReads
sincei.scFilterBarcodes
sincei.scFilterStats
sincei.scJSD
sincei.sincei
sincei.TopicModels
sincei.Utilities
sincei.WriteBedGraph
multiModal_clustering() (in module sincei.multimodalClustering)
N
natural_parametrization() (sincei.ExponentialFamily.Bernoulli method)
(sincei.ExponentialFamily.Beta method)
(sincei.ExponentialFamily.ExponentialFamily method)
(sincei.ExponentialFamily.Gamma method)
(sincei.ExponentialFamily.Gaussian method)
(sincei.ExponentialFamily.LogNormal method)
(sincei.ExponentialFamily.Poisson method)
(sincei.ExponentialFamily.SigmoidBeta method)
numberOfProcessors() (in module sincei.ParserCommon)
O
OffsetFragment (class in sincei.scBulkCoverage)
otherOptions() (in module sincei.ParserCommon)
P
parse_arguments() (in module sincei.sincei)
parseArguments() (in module sincei.scBAMops)
(in module sincei.scBulkCoverage)
(in module sincei.scClusterCells)
(in module sincei.scCombineCounts)
(in module sincei.scCountQC)
(in module sincei.scCountReads)
(in module sincei.scFilterBarcodes)
(in module sincei.scFilterStats)
(in module sincei.scJSD)
plotOptions() (in module sincei.ParserCommon)
Poisson (class in sincei.ExponentialFamily)
process_args() (in module sincei.ParserCommon)
(in module sincei.sincei)
R
readOptions() (in module sincei.ParserCommon)
remove_row_of_zeros() (in module sincei.ReadCounter)
run() (sincei.ReadCounter.CountReadsPerBin method)
(sincei.WriteBedGraph.WriteBedGraph method)
runLDA() (sincei.TopicModels.TOPICMODEL method)
runLSA() (sincei.TopicModels.TOPICMODEL method)
S
scaleCoverage() (in module sincei.WriteBedGraph)
shiftRead() (in module sincei.scBAMops)
show_or_hide() (in module sincei.ParserCommon)
SigmoidBeta (class in sincei.ExponentialFamily)
sincei
module
sincei.ExponentialFamily
module
sincei.FragmentFFT
module
sincei.GetStats
module
sincei.GLMPCA
module
sincei.multimodalClustering
module
sincei.ParserCommon
module
sincei.ReadCounter
module
sincei.RegionQuery
module
sincei.scBAMops
module
sincei.scBulkCoverage
module
sincei.scClusterCells
module
sincei.scCombineCounts
module
sincei.scCountQC
module
sincei.scCountReads
module
sincei.scFilterBarcodes
module
sincei.scFilterStats
module
sincei.scJSD
module
sincei.sincei
module
sincei.TopicModels
module
sincei.Utilities
module
sincei.WriteBedGraph
module
smartLabel() (in module sincei.ParserCommon)
smartLabels() (in module sincei.ParserCommon)
sufficient_statistics() (sincei.ExponentialFamily.Bernoulli method)
(sincei.ExponentialFamily.Beta method)
(sincei.ExponentialFamily.ExponentialFamily method)
(sincei.ExponentialFamily.Gamma method)
(sincei.ExponentialFamily.Gaussian method)
(sincei.ExponentialFamily.LogNormal method)
(sincei.ExponentialFamily.Poisson method)
T
Tester (class in sincei.ReadCounter)
TOPICMODEL (class in sincei.TopicModels)
transform() (sincei.GLMPCA.GLMPCA method)
U
umap_aligned() (in module sincei.multimodalClustering)
V
validateInputs() (in module sincei.ParserCommon)
W
WriteBedGraph (class in sincei.WriteBedGraph)
writeBedGraph_worker() (sincei.WriteBedGraph.WriteBedGraph method)
writeBedGraph_wrapper() (in module sincei.WriteBedGraph)
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