Files in CostaLab/sigurd
Single cell Genotyping Using RNA Data

DESCRIPTION

NAMESPACE

R/AllelFrequencyFoldChange.R R/AmpliconSupplementing.R R/CalculateAlleleFrequency.R R/CalculateAltReads.R R/CalculateConsensus.R R/CalculateCorrelationPValue.R R/CalculateCoverage.R R/CalculateFisherTestPValue.R R/CalculateForwardReads.R R/CalculateQuality.R R/CalculateRefReads.R R/CalculateReverseReads.R R/CalculateStrandCorrelation.R R/CallSupport.R R/ClonalDefinition.R R/ClonalDiversity.R R/CombineSEobjects.R R/Enrichment_Fisher.R R/Filtering.R R/Filtering_VAF_Threshold.R R/GetCellInfoPerVariant.R R/GetVariantInfo.R R/HeatmapVOI.R R/LoadingMAEGATK_typewise.R R/LoadingMGATK_typewise.R R/LoadingRawMatrix_typewise.R R/LoadingVCF_typewise.R R/LoadingVarTrix_typewise.R R/Merging_SE_list.R R/RowWiseSplit.R R/SeparatingMatrixToList.R R/SetVariantInfo.R R/UMIQC.R R/UMI_seq.R R/VariantBurden.R R/VariantCloneSizeThresholding.R R/VariantCorrelationHeatmap.R R/VariantFisherTestHeatmap.R R/VariantQuantileThresholding_Combined.R R/VariantSelection_Group.R R/VariantSelection_Quantile.R R/VariantSelection_TopCells.R R/VariantSelection_VMR.R R/VariantSelection_VMR_Group.R R/VariantWiseCorrelation.R R/VariantWiseFisherTest.R R/char_to_numeric.R R/combine_NAMES.R R/combine_SparseMatrix.R R/computeAFMutMatrix.R R/getAltMatrix.R R/getMutMatrix.R R/getReadMatrix.R R/getRefMatrix.R R/get_consensus.R R/load_object.R R/save_object.R R/sdiv.R README.md

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docs/deps/font-awesome-6.4.2/webfonts/fa-regular-400.ttf

docs/deps/font-awesome-6.4.2/webfonts/fa-regular-400.woff2

docs/deps/font-awesome-6.4.2/webfonts/fa-solid-900.ttf

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docs/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.ttf

docs/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.woff2

docs/deps/headroom-0.11.0/headroom.min.js

docs/deps/headroom-0.11.0/jQuery.headroom.min.js

docs/deps/jquery-3.6.0/jquery-3.6.0.js

docs/deps/jquery-3.6.0/jquery-3.6.0.min.js

docs/deps/jquery-3.6.0/jquery-3.6.0.min.map

docs/deps/search-1.0.0/autocomplete.jquery.min.js

docs/deps/search-1.0.0/fuse.min.js

docs/deps/search-1.0.0/mark.min.js

docs/index.html

docs/katex-auto.js

docs/lightswitch.js

docs/link.svg

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/AllelFrequencyFoldChange.html

docs/reference/AmpliconSupplementing.html

docs/reference/AmpliconSupplementing_big.html

docs/reference/CalculateAlleleFrequency.html

docs/reference/CalculateAltReads.html

docs/reference/CalculateConsensus.html

docs/reference/CalculateCorrelationPValue.html

docs/reference/CalculateCoverage.html

docs/reference/CalculateFisherTestPValue.html

docs/reference/CalculateFisherTestPValue2.html

docs/reference/CalculateForwardReads.html

docs/reference/CalculateQuality.html

docs/reference/CalculateRefReads.html

docs/reference/CalculateReverseReads.html

docs/reference/CalculateStrandCorrelation.html

docs/reference/CallSupport.html

docs/reference/ClonalDefinition.html

docs/reference/ClonalDiversity.html

docs/reference/CombineSEobjects.html

docs/reference/CombineSEobjects_big.html

docs/reference/Enrichment_FisherTest.html

docs/reference/Filtering.html

docs/reference/Filtering_big.html

docs/reference/GetCellInfoPerVariant.html

docs/reference/GetVariantInfo.html

docs/reference/HeatmapVoi.html

docs/reference/LoadingMAEGATK_typewise.html

docs/reference/LoadingMGATK_typewise.html

docs/reference/LoadingRawMatrix_typewise.html

docs/reference/LoadingVCF_typewise.html

docs/reference/LoadingVarTrix.html

docs/reference/LoadingVarTrix_ori.html

docs/reference/LoadingVarTrix_typewise.html

docs/reference/LoadingVarTrix_typewise_big.html

docs/reference/Merging_SE_list.html

docs/reference/RowWiseSplit.html

docs/reference/Rplot001.png

docs/reference/SeparatingMatrixToList.html

docs/reference/SetVariantInfo.html

docs/reference/UMIQC.html

docs/reference/UMI_seq.html

docs/reference/VariantBurden.html

docs/reference/VariantBurden_big.html

docs/reference/VariantCloneSizeThresholding.html

docs/reference/VariantCorrelationHeatmap.html

docs/reference/VariantFisherTestHeatmap.html

docs/reference/VariantQuantileThresholding.html

docs/reference/VariantQuantileThresholding_Combined.html

docs/reference/VariantSelection_Group.html

docs/reference/VariantSelection_Quantile.html

docs/reference/VariantSelection_TopCells.html

docs/reference/VariantSelection_VMR.html

docs/reference/VariantWiseCorrelation.html

docs/reference/VariantWiseFisherTest.html

docs/reference/char_to_numeric.html

docs/reference/combine_NAMES.html

docs/reference/combine_SparseMatrix.html

docs/reference/computeAFMutMatrix.html

docs/reference/getAltMatrix.html

docs/reference/getMutMatrix.html

docs/reference/getReadMatrix.html

docs/reference/getRefMatrix.html

docs/reference/get_consensus.html

docs/reference/ggsci_pal.html

docs/reference/index.html

docs/reference/load_object.html

docs/reference/save_object.html

docs/reference/sdiv.html

docs/search.json

docs/sitemap.xml

inst/extdata/CosmicSubset_filtered.vcf

inst/extdata/Input_Example_local.csv

inst/extdata/JAK2V617F.vcf

inst/extdata/MT_Input_VCF_NoMAF_Filtering.vcf

inst/extdata/chrM_Input_VCF_NoMAF_Filtering.vcf

man/AllelFrequencyFoldChange.Rd man/AmpliconSupplementing.Rd man/CalculateAlleleFrequency.Rd man/CalculateAltReads.Rd man/CalculateConsensus.Rd man/CalculateCorrelationPValue.Rd man/CalculateCoverage.Rd man/CalculateFisherTestPValue.Rd man/CalculateForwardReads.Rd man/CalculateQuality.Rd man/CalculateRefReads.Rd man/CalculateReverseReads.Rd man/CalculateStrandCorrelation.Rd man/CallSupport.Rd man/ClonalDefinition.Rd man/ClonalDiversity.Rd man/CombineSEobjects.Rd man/Enrichment_FisherTest.Rd man/Filtering.Rd man/Filtering_VAF_Threshold.Rd man/GetCellInfoPerVariant.Rd man/GetVariantInfo.Rd man/HeatmapVoi.Rd man/LoadingMAEGATK_typewise.Rd man/LoadingMGATK_typewise.Rd man/LoadingRawMatrix_typewise.Rd man/LoadingVCF_typewise.Rd man/LoadingVarTrix_typewise.Rd man/Merging_SE_list.Rd man/RowWiseSplit.Rd man/SeparatingMatrixToList.Rd man/SetVariantInfo.Rd man/UMIQC.Rd man/UMI_seq.Rd man/VariantBurden.Rd man/VariantCloneSizeThresholding.Rd man/VariantCorrelationHeatmap.Rd man/VariantFisherTestHeatmap.Rd man/VariantQuantileThresholding_Combined.Rd man/VariantSelection_Group.Rd man/VariantSelection_Quantile.Rd man/VariantSelection_TopCells.Rd man/VariantSelection_VMR.Rd man/VariantSelection_VMR_Group.Rd man/VariantWiseCorrelation.Rd man/VariantWiseFisherTest.Rd man/char_to_numeric.Rd man/combine_NAMES.Rd man/combine_SparseMatrix.Rd man/computeAFMutMatrix.Rd man/getAltMatrix.Rd man/getMutMatrix.Rd man/getReadMatrix.Rd man/getRefMatrix.Rd man/get_consensus.Rd man/load_object.Rd man/save_object.Rd man/sdiv.Rd

preprocessing/CandidateVariantAcquisition/CandidateVariantAcquisition.sh

preprocessing/CandidateVariantAcquisition/Example_COSMIC_IDs.tsv

preprocessing/CandidateVariantAcquisition/Example_Genes_Of_Interest.tsv

preprocessing/CandidateVariantAcquisition/Example_Histologies_Of_Interest.tsv

preprocessing/CandidateVariantAcquisition/Example_Regions_Of_Interest.tsv

preprocessing/MAESTER_Preprocessing/AssembleFASTQ.R

preprocessing/MAESTER_Preprocessing/MAESTER_Preprocessing.sh

preprocessing/VarTrix_Preprocessing/Get_Reads_Per_Molecule.py

preprocessing/VarTrix_Preprocessing/VarTrix_Preprocessing.sh

sigurd.Rproj

tests/testthat/test_data/Filtering_Alts_Threshold_ExpectedResults.rds

tests/testthat/test_data/Filtering_Blacklist_ExpectedResults.rds

tests/testthat/test_data/Filtering_Blacklisted_Barcodes.tsv

tests/testthat/test_data/Filtering_CellThreshold_ExpectedResults.rds

tests/testthat/test_data/Filtering_Fraction_Threshold_ExpectedResults.rds

tests/testthat/test_data/Filtering_VariantThreshold_ExpectedResults.rds

tests/testthat/test_data/LoadingMAEGATK_typewise_Test_Barcodes.tsv

tests/testthat/test_data/LoadingMAEGATK_typewise_Test_Data.rds

tests/testthat/test_data/LoadingMAEGATK_typewise_Test_ExpectedResults.rds

tests/testthat/test_data/MAEGATK_inputfile_test.csv

tests/testthat/test_data/Merging_SE_list_ExpectedResults.rds

tests/testthat/test_data/VCF_Test/VCF_ExpectedResults.rds

tests/testthat/test_data/VCF_Test/VCF_inputfile_test.csv

tests/testthat/test_data/VCF_Test/cellSNP.base.vcf

tests/testthat/test_data/VCF_Test/cellSNP.cells.vcf

tests/testthat/test_data/VCF_Test/cellSNP.samples.tsv

tests/testthat/test_data/VCF_Test/cellSNP.tag.AD.mtx

tests/testthat/test_data/VCF_Test/cellSNP.tag.DP.mtx

tests/testthat/test_data/VCF_Test/cellSNP.tag.OTH.mtx

tests/testthat/test_data/VCF_Test/test.vcf

tests/testthat/test_data/VarTrix_Test/SNV.loci.txt

tests/testthat/test_data/VarTrix_Test/Test/out_matrix_consensus.mtx

tests/testthat/test_data/VarTrix_Test/Test/out_matrix_coverage.mtx

tests/testthat/test_data/VarTrix_Test/Test/ref_matrix_coverage.mtx

tests/testthat/test_data/VarTrix_Test/barcodes.tsv

tests/testthat/test_data/VarTrix_Test/inputfile_test.csv

tests/testthat/test_data/VarTrix_Test/test.rds

tests/testthat/test_data/VarTrix_Test/test.vcf

tests/testthat/test_data/test.bam

tests/testthat/test_data/test.bam.bai

tutorials/10X_CellMixture_SIGURD.Rmd tutorials/BoneMarrow_SIGURD.R tutorials/MPN_SIGURD.R tutorials/SW_CellMixture_SIGURD.Rmd tutorials/comparison/10X_CellMixture.Rmd tutorials/comparison/BoneMarrow.Rmd tutorials/comparison/SW_CellMixture.Rmd vignettes/BoneMarrow_SIGURD.Rmd vignettes/MPN_SIGURD.Rmd vignettes/SW_CellMixture_SIGURD.Rmd vignettes/TenX_CellMixture_SIGURD.Rmd

CostaLab/sigurd documentation built on Feb. 10, 2025, 11:08 p.m.

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CostaLab/sigurd
Single cell Genotyping Using RNA Data

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CostaLab/sigurd Single cell Genotyping Using RNA Data

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CostaLab/sigurd
Single cell Genotyping Using RNA Data

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Single cell Genotyping Using RNA Data