Function reference
-
fastReseg_flag_all_errors()
- fastReseg_flag_all_errors
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fastReseg_full_pipeline()
- fastReseg_full_pipeline
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fastReseg_perFOV_full_process()
- fastReseg_perFOV_full_process
-
runPreprocess()
- runPreprocess
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get_baselineCT()
- get_baselineCT
-
choose_distance_cutoff()
- choose_distance_cutoff
-
estimate_MeanProfile()
- estimate_MeanProfile
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scoreGenesInRef()
- scoreGenesInRef
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getCellType_maxScore()
- getCellType_maxScore
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getScoreCellType_gene()
- getScoreCellType_gene
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example_CellGeneExpr
- per cell gene expression matrix based on raw transcript data files generated by SMI
-
example_baselineCT
- Percentile profile for single cell distribution of transcript number and average tLLR score from example dataset for spatial transcriptional profiling of tissue
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example_clust
- Cluster assignment for cells based on per cell gene expression profile and reference profiles in example data set
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example_refProfiles
- Data for cell type specific reference profiles
-
mini_transcriptDF
- Transcript level data frame from Example dataset for spatial transcriptional profiling of tissue
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ori_CellStatsDF
- Cell level data frame from Example dataset for spatial transcriptional profiling of tissue
-
ori_RawExprs
- Cell x Gene expression matrix from Example dataset for spatial transcriptional profiling of tissue
-
runPreprocess()
- runPreprocess
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runSegErrorEvaluation()
- runSegErrorEvaluation
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runTranscriptErrorDetection()
- runTranscriptErrorDetection
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runSegRefinement()
- runSegRefinement
-
runSegErrorEvaluation()
- runSegErrorEvaluation
-
score_cell_segmentation_error()
- score_cell_segmentation_error
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runTranscriptErrorDetection()
- runTranscriptErrorDetection
-
flag_bad_transcripts()
- flag_bad_transcripts
-
groupTranscripts_dbscan()
- groupTranscripts_dbscan
-
groupTranscripts_Delaunay()
- groupTranscripts_Delaunay
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createSpatialDelaunayNW_from_spatLocs()
- createSpatialDelaunayNW_from_spatLocs
-
flagTranscripts_LDA_hyperplane()
- flagTranscripts_LDA_hyperplane
Segmentation refinement
Functions to evaluate neighborhood of flagged transcript groups and perform refinement
-
runSegRefinement()
- runSegRefinement
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prepResegDF()
- prepResegDF
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get_neighborhood_content()
- get_neighborhood_content
-
getNeighbors_transDF()
- getNeighbors_transDF
-
decide_ReSegment_Operations()
- decide_ReSegment_Operations
-
update_transDF_ResegActions()
- update_transDF_ResegActions
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transDF_to_perCell_data()
- transDF_to_perCell_data
Visualization
Auxillary function to visualize spatial pattern of transcript-level information of multiple cells
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plotSpatialScoreMultiCells()
- plotSpatialScoreMultiCells
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numCores()
- Get number of cores for parallelized operations
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checkTransFileInputsAndLoadFirst()
- checkTransFileInputsAndLoadFirst
-
prepare_perFOV_transDF()
- prepare_perFOV_transDF
-
myFun_fov_load()
- myFun_fov_load
-
check_config_leiden()
- check_config_leiden
-
check_config_spatialNW()
- check_config_spatialNW
-
checkAndPrepInputs_perFOV()
- checkAndPrepInputs_perFOV
-
checkTypeLengthValue()
- checkTypeLengthValue
-
compartment_and_add_extra()
- compartment_and_add_extra
-
initializeAllSegRes()
- initializeAllSegRes
-
makeDummyOuts_perFOV()
- makeDummyOuts_perFOV
-
myFun_3point_singleCell()
- myFun_3point_singleCell