VariantTools: Tools for Working with Genetic Variants

Tools for detecting, filtering, calling, comparing and plotting variants.

AuthorMichael Lawrence, Jeremiah Degenhardt, Robert Gentleman
Date of publicationNone
MaintainerMichael Lawrence <michafla@gene.com>
LicenseArtistic-2.0
Version1.16.0

View on Bioconductor

Files in this package

VariantTools/.BBSoptions
VariantTools/DESCRIPTION
VariantTools/NAMESPACE
VariantTools/NEWS
VariantTools/R
VariantTools/R/apply.R VariantTools/R/callGenotypes.R VariantTools/R/callVariants.R VariantTools/R/callableGenes.R VariantTools/R/cgpGr2Vcf.R VariantTools/R/diagnostics.R VariantTools/R/fisher_p.R VariantTools/R/idVerify.R VariantTools/R/pileupVariants.R VariantTools/R/postFilterVariants.R VariantTools/R/qaVariants.R VariantTools/R/sampleSpecific.R VariantTools/R/setops.R VariantTools/R/tallyVariants.R VariantTools/R/test_VariantTools_package.R VariantTools/R/transcript2genome.R VariantTools/R/utils.R VariantTools/R/variantConcordance.R VariantTools/R/wildtype.R
VariantTools/build
VariantTools/build/vignette.rds
VariantTools/inst
VariantTools/inst/doc
VariantTools/inst/doc/VariantTools.R
VariantTools/inst/doc/VariantTools.Rnw
VariantTools/inst/doc/VariantTools.pdf
VariantTools/inst/unitTests
VariantTools/inst/unitTests/test_calculateConcordanceMatrix.R
VariantTools/inst/unitTests/test_idVerify.R
VariantTools/inst/unitTests/test_variantConcordance.R
VariantTools/inst/vcf
VariantTools/inst/vcf/header.csv
VariantTools/man
VariantTools/man/FilterConstructors.Rd VariantTools/man/annnotateWithControlDepth.Rd VariantTools/man/callGenotypes.Rd VariantTools/man/callSampleSpecificVariants.Rd VariantTools/man/callVariants.Rd VariantTools/man/callWildtype.Rd VariantTools/man/concordance.Rd VariantTools/man/extractCoverageForPositions.Rd VariantTools/man/matchVariants.Rd VariantTools/man/pileupVariants.Rd VariantTools/man/postFilterVariants.Rd VariantTools/man/qaVariants.Rd VariantTools/man/tallyVariants.Rd VariantTools/man/variantGR2Vcf.Rd
VariantTools/oldman
VariantTools/oldman/TwoSampleFET.Rd
VariantTools/oldman/VEP2gr.Rd
VariantTools/oldman/annotateTrans.Rd
VariantTools/oldman/detectQuality.Rd
VariantTools/oldman/isCallable.Rd
VariantTools/oldman/plotTitv.Rd
VariantTools/oldman/variantConcordance.Rd
VariantTools/oldman/wildtype.Rd
VariantTools/scripts
VariantTools/scripts/APC_EXvR_freq.pdf
VariantTools/scripts/ATM_EXvR_freq.pdf
VariantTools/scripts/KRAS_EXvR_freq.pdf
VariantTools/scripts/KRAS_LOH.pdf
VariantTools/scripts/N_NS_RNA_EX.R
VariantTools/scripts/RAS_PATH_MUT.pdf
VariantTools/scripts/README
VariantTools/scripts/R_segfault.R
VariantTools/scripts/SNVsOmuC.Rnw
VariantTools/scripts/TN_FET.R
VariantTools/scripts/TP53_EXvR_freq.pdf
VariantTools/scripts/arraySNP_v_seq.R
VariantTools/scripts/array_het.R
VariantTools/scripts/byCoverage.R
VariantTools/scripts/check_consequences.R
VariantTools/scripts/check_damaging.R
VariantTools/scripts/check_freq_rna_ex.R
VariantTools/scripts/example_runs
VariantTools/scripts/example_runs/SAM587376_run.sh
VariantTools/scripts/example_runs/SAM587376_run_TN.sh
VariantTools/scripts/example_runs/SAM587376_varEff.sh
VariantTools/scripts/functional_vep.R
VariantTools/scripts/gastric.R
VariantTools/scripts/getAlleleByLocus_mod.R
VariantTools/scripts/getChrGRangesFromGmap.Rd
VariantTools/scripts/make_RNA_EX_gene_plot.R
VariantTools/scripts/mkRuns.R
VariantTools/scripts/mk_RASPath_gene_plot.R
VariantTools/scripts/old.variantFilter.R
VariantTools/scripts/plot_help.R
VariantTools/scripts/prob_base.R
VariantTools/scripts/rnaValRate.R
VariantTools/scripts/rnaValWrapper.R
VariantTools/scripts/run_TN_wrapper.R
VariantTools/scripts/run_callVar_wrapper.R
VariantTools/scripts/temp.R
VariantTools/scripts/testing_Rsamtools.R
VariantTools/scripts/testing_mclapply.R
VariantTools/scripts/tumor_variant_plot.R
VariantTools/scripts/variantFilter_OLD.R
VariantTools/scripts/wrap_annotate_trans.R
VariantTools/tests
VariantTools/tests/VariantTools_unit_tests.R
VariantTools/vignettes
VariantTools/vignettes/VariantTools.Rnw

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

All documentation is copyright its authors; we didn't write any of that.